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MD5sum: bb119c9296af5c6ebd3ae703b35fdb64 Package: alabaster.string Version: 1.7.0 Depends: Biostrings, alabaster.base Imports: utils, methods, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, testthat License: MIT + file LICENSE MD5sum: f9ec0963858c33bc4414f4b547096807 Package: ALDEx2 Version: 1.39.0 Depends: methods, stats, zCompositions, lattice, latticeExtra Imports: Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest, directlabels Suggests: testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick License: GPL (>= 3) MD5sum: 6c818b88ea0ee4b4cfe1a07d03659e63 Package: alevinQC Version: 1.23.1 Depends: R (>= 4.0) Imports: rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0), GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils, tximport (>= 1.17.4), cowplot, rlang, Rcpp LinkingTo: Rcpp Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager License: MIT + file LICENSE MD5sum: 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rmarkdown, testthat, tidyr, tidyverse License: Artistic-2.0 MD5sum: a44f8e4631ef0eee1c8e0ff282bb3a47 Package: ANF Version: 1.29.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 7e4eb76b865d9aef98f18ac224ae02e0 Package: annaffy Version: 1.79.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: 435f93f46d63402a54d9d6a59d91452d Package: annmap Version: 1.49.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: d9bc1fb984a9681f2cfc053197a73cf4 Package: annotate Version: 1.85.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 8f0fe5870ca380cae915d78b0bd53d07 Package: AnnotationDbi Version: 1.69.0 Depends: R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: 4f5254559b43ed10e6c3ceb672db67c3 Package: AnnotationFilter Version: 1.31.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 803dd58ecdbed12a9c8ccfc636f1a718 Package: AnnotationForge Version: 1.49.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 MD5sum: facdf025b0a44c8f8503b8d7a2d2f112 Package: AnnotationHub Version: 3.15.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 34fb4bbf378b4756388fdc9d020374ad Package: annotationTools Version: 1.81.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: e6082bfa6540ac58e1ca6833e3266931 Package: anota Version: 1.55.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 5e871b27c319bc5b7dcaa6f64ec535c9 Package: antiProfiles Version: 1.47.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: 626edc43af4a026dde85f239acfbebbc Package: AnVIL Version: 1.19.5 Depends: R (>= 3.6), dplyr, AnVILBase Imports: stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), yaml, tibble, tidyselect, tidyr, rlang, shiny, DT, miniUI, htmltools, BiocBaseUtils Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle License: Artistic-2.0 MD5sum: a67fa0672b03f4403026811ca07bc9bf Package: AnVILAz Version: 1.1.0 Imports: AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods, rjsoncons, tibble, utils Suggests: BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 0c0fecb2e494d21c5de84f78de7e6023 Package: AnVILBase Version: 1.1.0 Imports: httr, httr2, dplyr, jsonlite, methods, tibble Suggests: AnVIL, AnVILAz, AnVILGCP, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), tinytest License: Artistic-2.0 MD5sum: f166e03bb091916f56698fa44b04220f Package: AnVILBilling Version: 1.17.0 Depends: R (>= 4.1) Imports: methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr, dplyr, lubridate, plotly, ggplot2 Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 533ee2e0d2ccb71d13b211c4b79c3920 Package: AnVILGCP Version: 1.1.2 Imports: AnVILBase, BiocBaseUtils, dplyr, httr, jsonlite, methods, rlang, stats, tibble, tidyr, utils Suggests: AnVIL, BiocStyle, knitr, rmarkdown, testthat, withr License: Artistic-2.0 MD5sum: b1b5a633e8e9c016a6e39adb63fe489b Package: AnVILPublish Version: 1.17.0 Imports: AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 31021eb0785317ee58772812302aa9f8 Package: AnVILWorkflow Version: 1.7.2 Depends: R (>= 4.4.0), AnVILGCP, AnVILBase, httr Imports: AnVIL, dplyr, jsonlite, rlang, tibble, tidyr, utils, methods, plyr, stringr Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: bb5c0c15c4a5bd34aa79fad664a2ab91 Package: apComplex Version: 2.73.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 0467980cd02701cb701e2ce0248f2729 Package: apeglm Version: 1.29.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 6009fa4db0038c02de0382ccc45a5346 Package: APL Version: 1.11.2 Depends: R (>= 4.4.0) Imports: Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly, SeuratObject, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, sparseMatrixStats, testthat License: GPL (>= 3) MD5sum: c3cd7a4e95f455a7347b301506d1c14c Package: aroma.light Version: 3.37.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) MD5sum: 661baa6d070aa45b524112dbfc9252f3 Package: arrayMvout Version: 1.65.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy Imports: mdqc, affyContam, lumi Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 MD5sum: 17a9369d31cfe4707ad3645dcfa7910c Package: arrayQuality Version: 1.85.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: 2c1c9963a4b97d797ef229019ac07360 Package: arrayQualityMetrics Version: 3.63.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn (>= 3.23.3), XML, svglite Suggests: ALLMLL, CCl4, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 9c0486f157bece4dd6740205d2dccada Package: ARRmNormalization Version: 1.47.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 MD5sum: 5511d09251bf2f69f27b85622d4ade3c Package: artMS Version: 1.25.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, bit64, circlize, cluster, corrplot, data.table, dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: f6fbf21595e268e3765da8bb7de73fd9 Package: ASAFE Version: 1.33.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 78fb6c521e42ad9216f697cadfce282e Package: ASEB Version: 1.51.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 7e3073ddff16258ff454d3e577a27dd2 Package: ASGSCA Version: 1.41.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 8b920e6a537cc72c8fb7e53e7fd7ac9c Package: ASICS Version: 2.23.0 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) MD5sum: a858b7d033cfc701f25644cd6c84414b Package: ASpli Version: 2.17.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply, txdbmaker License: GPL MD5sum: c6194875f52c56751899c68701bfa8fa Package: ASSET Version: 2.25.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: 6c6f78207f4c60c9ffc7d1cb3a29ad07 Package: ASSIGN Version: 1.43.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 6f8e89e8be1a1f56eae8e2815e0422f5 Package: assorthead Version: 1.1.13 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: abbf21a1df228a09c14b90426ce22fad Package: ASURAT Version: 1.11.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 03c4d9983922909722e621cc2d602d6f Package: atena Version: 1.13.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: 0ba3c4cf5808e0ef3bbc9d4cb11a78fc Package: atSNP Version: 1.23.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: b25bfafacf0550b646ecd5d526232c05 Package: attract Version: 1.59.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: 86dce642c3616ddc4045cd561482edc1 Package: AUCell Version: 1.29.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: b295457e0aed0c98d935b537e8c7541b Package: autonomics Version: 1.15.102 Depends: R (>= 4.0) Imports: abind, BiocFileCache, BiocGenerics, bit64, cluster, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, survival, tidyr, tidyselect, tools, utils, vsn Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, Biobase, BiocManager, BiocStyle, Biostrings, coin, diagram, DBI, e1071, ensembldb, GenomicDataCommons, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, jsonlite, knitr, lme4, lmerTest, MASS, patchwork, mixOmics, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, testthat, UniProt.ws, writexl, XML License: GPL-3 MD5sum: 011ad9aa2c0d24682d1ae4810e6b1faf Package: AWFisher Version: 1.21.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: 12d4c22b2bb628d1b1201e8aa651171a Package: awst Version: 1.15.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: b06a91f59907f558a4ba1d37bfde4c78 Package: BaalChIP Version: 1.33.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 25b401cb668292350a8b7d3d6b85366d Package: bacon Version: 1.35.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: ba9ebd8c3735fd5b47bb14e3249067d4 Package: BAGS Version: 2.47.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: aabf53c4817e47f949d6e168701dddb5 Package: bambu Version: 3.9.0 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 88e4c1b4cbe9efc65d4345a77a091957 Package: bamsignals Version: 1.39.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: ee311aa81b67d1ffe75088c0e838efc6 Package: BANDITS Version: 1.23.0 Depends: R (>= 4.3.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: 8a9360f3687d1b1170d4c7b17f18dd61 Package: bandle Version: 1.11.0 Depends: R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc Imports: Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>= 0.19-4) LinkingTo: Rcpp, RcppArmadillo, BH Suggests: testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: 62ff5d78f670d78a8d56989ef421bccd Package: banocc Version: 1.31.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 0eedc7e88a13a62e4df0086bf451379d Package: barcodetrackR Version: 1.15.0 Depends: R (>= 4.1) Imports: cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges, graphics, grDevices, magrittr, plyr, proxy, RColorBrewer, rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors, tibble, tidyr, vegan, viridis, utils Suggests: BiocStyle, knitr, magick, rmarkdown, testthat License: file LICENSE MD5sum: 7d61a76dc9c9c45d143a5038edee110e Package: basecallQC Version: 1.31.0 Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) MD5sum: a4a22b67a3d9e0840742bfb5ce53ab59 Package: BaseSpaceR Version: 1.51.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: 1427cd4c660306e75d16385f6b3f0fdb Package: Basic4Cseq Version: 1.43.0 Depends: R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: cc2a37f11d6a61b52bb37665559c2aad Package: BasicSTARRseq Version: 1.35.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats Suggests: knitr License: LGPL-3 MD5sum: 24692b1b6b41260575366cd1a11fe49f Package: basilisk Version: 1.19.0 Depends: reticulate Imports: utils, methods, parallel, dir.expiry, basilisk.utils (>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: 18a84bf9522cca4349e93242e7c04001 Package: basilisk.utils Version: 1.19.0 Imports: utils, methods, tools, dir.expiry Suggests: reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk License: GPL-3 MD5sum: b4c5a57dfaf2bd16ec0b5cfacfc2f55d Package: batchelor Version: 1.23.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, SparseArray, DelayedArray (>= 0.31.5), DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 MD5sum: f560fbdf4815e035f26c4ced8ae90cbb Package: BayesKnockdown Version: 1.33.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: 2dbd3e55ee65e15a29d7ae8c6131a630 Package: bayNorm Version: 1.25.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 8a7a8124e9ed3c3c4c6301ed25aca9a4 Package: baySeq Version: 2.41.0 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 4ecd4cd30b2f54ab6748d12432455cad Package: BCRANK Version: 1.69.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: 3265a6773fd34882da32c409a33f0eb2 Package: bcSeq Version: 1.29.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: ac8b1d6e412c791a28716f09dcd8c039 Package: beachmat Version: 2.23.6 Imports: methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics, Matrix, Rcpp LinkingTo: Rcpp, assorthead Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array, beachmat.hdf5 License: GPL-3 MD5sum: 713b56884a6e1fc67bd084b23b8089ac Package: 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cowplot, data.table, scales, stats, Matrix Suggests: knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR License: Artistic-2.0 MD5sum: c37bc8d1e5a99647ffe220f9a67da369 Package: BioNERO Version: 1.15.0 Depends: R (>= 4.1) Imports: WGCNA, dynamicTreeCut, ggdendro, matrixStats, sva, RColorBrewer, ComplexHeatmap, ggplot2, rlang, ggrepel, patchwork, reshape2, igraph, ggnetwork, intergraph, NetRep, stats, grDevices, utils, methods, BiocParallel, minet, GENIE3, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr License: GPL-3 MD5sum: 5560100dd68d21c4bd4b9aeb91163b54 Package: BioNet Version: 1.67.0 Depends: R (>= 2.10.0), graph, RBGL Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) MD5sum: f7227f278ec1a91686cde739def7c3f1 Package: BioQC Version: 1.35.0 Depends: R (>= 3.5.0), Biobase Imports: edgeR, Rcpp, methods, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer License: GPL (>= 3) + file LICENSE MD5sum: a120baff1e16c8eb29fe156776df3503 Package: Biostrings Version: 2.75.3 Depends: R (>= 4.0.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), XVector (>= 0.37.1), GenomeInfoDb Imports: methods, utils, grDevices, stats, crayon LinkingTo: S4Vectors, IRanges, XVector Suggests: graphics, pwalign, BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr, testthat (>= 3.0.0), covr License: Artistic-2.0 MD5sum: 336d542bae70b288b52dba8dc8d4c85d Package: 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RUnit, BiocGenerics License: GPL (>= 2) MD5sum: ced9d1efcbd388e6f0ac3aa4a1811a7f Package: BloodGen3Module Version: 1.15.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, ExperimentHub, methods, grid, graphics, stats, grDevices, circlize, testthat, ComplexHeatmap(>= 1.99.8), ggplot2, matrixStats, gtools, reshape2, preprocessCore, randomcoloR, V8, limma Suggests: RUnit, devtools, BiocGenerics, knitr, rmarkdown License: GPL-2 MD5sum: 2bdfe0f281dbed4cf0504e3db20557be Package: bluster Version: 1.17.0 Imports: stats, methods, utils, cluster, Matrix, Rcpp, igraph, S4Vectors, BiocParallel, BiocNeighbors LinkingTo: Rcpp, assorthead Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster, DirichletMultinomial, vegan, fastcluster License: GPL-3 MD5sum: 2c7cd3d596a96659fb10d14956dbe748 Package: bnbc Version: 1.29.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: 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borealis Version: 1.11.0 Depends: R (>= 4.2.0), Biobase Imports: doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist, bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot, dplyr, rlang, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL-3 MD5sum: 875c6ec67968c5b2fe9b95a1b8812dca Package: BPRMeth Version: 1.33.0 Depends: R (>= 3.5.0), GenomicRanges Imports: assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 365d0f9d0591a076d605a1b7a21842a7 Package: BRAIN Version: 1.53.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: f9791fc449000a10c0d46e12400f3a8d Package: 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SpatialExperiment, SummarizedExperiment, tools Suggests: knitr, markdown, rmarkdown, STexampleData, testthat (>= 3.0.0), codetools, Matrix, lattice, cluster, survival, MASS, nlme License: CeCILL | file LICENSE MD5sum: d807052e268bb27494a7145be4f3b544 Package: BUMHMM Version: 1.31.0 Depends: R (>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: 4538fdabbef048a5bf2d102fab4e0f02 Package: bumphunter Version: 1.49.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 7a69a8aacc390b069ef7054c574f6c0c Package: BumpyMatrix Version: 1.15.0 Imports: utils, methods, Matrix, 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BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE MD5sum: ce2efcf2dfdd29784e00057fc9517324 Package: BUSseq Version: 1.13.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 MD5sum: fc9fa10730c8848acbca1446940bc20f Package: CaDrA Version: 1.5.0 Depends: R (>= 4.4.0) Imports: doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) License: GPL-3 + file LICENSE MD5sum: 5c43292cabf35f060fb7dd2e8fa5e9f1 Package: CAEN Version: 1.15.0 Depends: R (>= 4.1) Imports: stats,PoiClaClu,SummarizedExperiment,methods Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle License: GPL-2 MD5sum: d049b138e1fb836534ef83a92f69c160 Package: cageminer Version: 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dplyr, tibble, tidyr, rjson, rmarkdown Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo License: GPL-3 MD5sum: 36babe02824e89516212c6c825ef7a80 Package: CATALYST Version: 1.31.2 Depends: R (>= 4.4), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, Matrix, matrixStats, methods, nnls, purrr, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: e323a3c254d6c0867abaebd240c2252b Package: Category Version: 2.73.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, 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BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: f705b2fc9e97e57cce9b0fc9686fe2d5 Package: cellity Version: 1.35.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 74500f69d735aafa7be984899ac4b40e Package: CellMapper Version: 1.33.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: 1dd357b3a78b87932d00e5af85b07d8d Package: cellmigRation Version: 1.15.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 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R.utils, shinyWidgets, colorspace, shinyhelper, shinycssloaders, ggnewscale, shinydashboard, DT, colourpicker, grDevices, methods, utils, stats, ggplot2, magrittr, tools Suggests: knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: b4517beef6890b56ca2b1bf4d19cdb9f Package: clippda Version: 1.57.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: 35e2b043be75ddaa448ddae32c60a687 Package: clipper Version: 1.47.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 MD5sum: 8d250a76d5cbf6712536c647bae0211f Package: cliqueMS Version: 1.21.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop, slam, matrixStats, methods LinkingTo: Rcpp, BH, RcppArmadillo Suggests: BiocParallel, knitr, rmarkdown, testthat, CAMERA License: GPL (>= 2) MD5sum: 399fc581055c0080ceadabca4ca9626d Package: Clomial Version: 1.43.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: 4087f851a8a029aca39e837b699fb002 Package: clst Version: 1.55.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: c7ed21c94f3a424e5dcaa80d3b271db2 Package: clstutils Version: 1.55.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit License: GPL-3 MD5sum: d9fa79ce6060733f1c592aa3b4cdcbf5 Package: ClustAll Version: 1.3.0 Depends: R (>= 4.2.0) Imports: FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 License: GPL-2 MD5sum: 6fa06a94c320cf3415f5ebb636e883bf Package: clustComp Version: 1.35.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: e5b5fc34fe48daab187f9712501db15b Package: clusterExperiment Version: 2.27.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 MD5sum: 80fb074a5f3a0c8b2aa9e7fd28e12acc Package: ClusterFoldSimilarity Version: 1.3.0 Imports: methods, igraph, ggplot2, scales, BiocParallel, graphics, stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat, SeuratObject, SingleCellExperiment, ggdendro Suggests: knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle License: Artistic-2.0 MD5sum: 0d92af1f97c256b1c5bef86952991ce9 Package: ClusterJudge Version: 1.29.1 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: 0056c7992b8ae62536d1196618020e4b Package: clusterProfiler Version: 4.15.1 Depends: R (>= 3.5.0) Imports: AnnotationDbi, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3), GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.1.6) Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat License: Artistic-2.0 MD5sum: 64bf8caaf8113774a6e4a9dde96c0584 Package: clusterSeq Version: 1.31.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 0610cf28c33be74e50e7dff809148423 Package: ClusterSignificance Version: 1.35.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: 99f792433628b77c0345913bd3a412a5 Package: clusterStab Version: 1.79.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: da345228997d926f272905e73c8f4511 Package: clustifyr Version: 1.19.0 Depends: R (>= 2.10) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE MD5sum: fb45e4813b35b64ab499cb98c32ede74 Package: ClustIRR Version: 1.5.39 Depends: R (>= 4.3.0) Imports: blaster, future, future.apply, grDevices, igraph, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork License: GPL-3 + file LICENSE MD5sum: e9a1394db39fa69a3c3d189499735a73 Package: CMA Version: 1.65.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: 6b78d718253dca986ed4b4d87d8439df Package: cmapR Version: 1.19.0 Depends: R (>= 4.0) Imports: methods, rhdf5, data.table, flowCore, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle, rmarkdown License: file LICENSE MD5sum: 4cf8f0084d77c893af3fd290205b65fb Package: cn.mops Version: 1.53.0 Depends: R (>= 3.5.0), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors Suggests: DNAcopy License: LGPL (>= 2.0) MD5sum: 321b1793879e5461c3c3366dde665e65 Package: CNAnorm Version: 1.53.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: 79cabb6fd5787515c8556962db8dab5a Package: CNORdt Version: 1.49.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 28c718d7272a40cd2408513bf377d9af Package: CNORfeeder Version: 1.47.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: 520cdd37b0ce6fcb7703522b64ad8697 Package: CNORfuzzy Version: 1.49.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: ef638146e0f7c3a9e007e5b134218886 Package: CNORode Version: 1.49.0 Depends: CellNOptR, genalg Suggests: knitr, rmarkdown Enhances: doParallel, foreach License: GPL-2 MD5sum: d043f884e5e9451e51a3fdf946ddab96 Package: CNTools Version: 1.63.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: ebe6171ed9e220ec029e272b9b90f186 Package: cnvGSA Version: 1.51.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: 96a82b6ae7be7de463e6ffa03246c64e Package: CNViz Version: 1.15.0 Depends: R (>= 4.0), shiny (>= 1.5.0) Imports: dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: adb71f0d646b468c7f20e9496b358470 Package: CNVMetrics Version: 1.11.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: e4f9cff9ff1c31c531b81ff42f9b564c Package: CNVPanelizer Version: 1.39.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: ad925c1b8a0369e3673372700a87ee71 Package: CNVRanger Version: 1.23.0 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod License: Artistic-2.0 MD5sum: ead120f290f1a7f0fe092e5b48055e27 Package: CoCiteStats Version: 1.79.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: d0d49edc01b0a908f6f56a2db943cdf4 Package: COCOA Version: 2.21.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: e8b6fbab96a846e85acdec188f6320d0 Package: codelink Version: 1.75.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: c39af08209cea18826efe2a61f7e67d2 Package: CODEX Version: 1.39.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: 4e1f0024e39fcfdb7f38057def621c8c Package: CoGAPS Version: 3.27.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache License: BSD_3_clause + file LICENSE MD5sum: 246b78d1ab5684155d65e29a46551657 Package: cogena Version: 1.41.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: 6d90aa37a192c030cf1a7e0d7851137c Package: cogeqc Version: 1.11.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: 4bc30ff70162bed3fa4c8b6c2931594b Package: Cogito Version: 1.13.0 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, GenomeInfoDb, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 576caf4942e4dc678d0ce9062269d8f7 Package: coGPS Version: 1.51.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: 1b090e6078af792bf624032c92d506ac Package: cola Version: 2.13.0 Depends: R (>= 4.0.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.5.4), matrixStats, GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6), digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 2e61c5975b4e132cd9bf6fa3c27a9a78 Package: comapr Version: 1.11.1 Depends: R (>= 4.1.0) Imports: methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod License: MIT + file LICENSE MD5sum: 4d902a751da866eef5e3a40385658140 Package: combi Version: 1.19.0 Depends: R (>= 4.0), DBI Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>= 1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 170246be26b07681633f959e880a66bd Package: coMethDMR Version: 1.11.0 Depends: R (>= 4.1) Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: GPL-3 MD5sum: 7f1ee6292916c3765af401ac1f1c588f Package: COMPASS Version: 1.45.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 MD5sum: 6b04d81e9cd8f772105da6fa081d1f85 Package: compcodeR Version: 1.43.0 Depends: R (>= 4.0), sm Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: ba9bacf9856dc735640e9c57cc9e5215 Package: compEpiTools Version: 1.41.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: eb52aaf07204f7a498b916212ee84278 Package: ComplexHeatmap Version: 2.23.0 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE MD5sum: 047841aae96ee9bc421dc55451ccc043 Package: CompoundDb Version: 1.11.2 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel, stringi Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: 5fac49ccdb53c56c870ffef4b4e1a7dd Package: ComPrAn Version: 1.15.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 93f450e185bbddbe6a211e4c3cbae4fb Package: compSPOT Version: 1.5.0 Depends: R (>= 4.3.0) Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3e295c59811c219653383c97cd152a60 Package: concordexR Version: 1.7.1 Depends: R (>= 4.4.0) Imports: BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli, DelayedArray, Matrix, methods, purrr, rlang, SingleCellExperiment, sparseMatrixStats, SpatialExperiment, SummarizedExperiment Suggests: BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 643aed06cd01ec58552c08c24ba6f9b8 Package: condiments Version: 1.15.1 Depends: R (>= 4.0) Imports: slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats License: MIT + file LICENSE MD5sum: 28fe7c7c8336b804cb26e172f908e972 Package: CONFESS Version: 1.35.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 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b637e3255ecac52406ab90df50c6cc23 Package: consICA Version: 2.5.0 Depends: R (>= 4.2.0) Imports: fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats, SummarizedExperiment, BiocParallel, graph, ggplot2, methods, Rfast, pheatmap, survival, topGO, graphics, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat License: MIT + file LICENSE MD5sum: bde82460c8cf0c5d2194bc46a5a8b814 Package: CONSTANd Version: 1.15.0 Depends: R (>= 4.1) Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma License: file LICENSE MD5sum: 963bec377cd164b9f8c0f30a29f33077 Package: convert Version: 1.83.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: 69d70179466823716a6e55340d60c0cb Package: copa Version: 1.75.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 MD5sum: b3b7f2628682d17705075d3dd0b5c0df Package: coRdon Version: 1.25.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, 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gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch License: GPL-3 MD5sum: e2edd5dab1d473dd529a11a5ad85cd77 Package: covEB Version: 1.33.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: e61313cba282ce99f62045e083584954 Package: covRNA Version: 1.33.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 1457995b6b0795c474a8242b0a09074f Package: cpvSNP Version: 1.39.0 Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: ed583341f11a36b923b65813b99fb3fe Package: cqn Version: 1.53.0 Depends: R (>= 2.10.0), mclust Imports: splines, graphics, nor1mix, stats, quantreg 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methods, S4Vectors, txdbmaker Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils License: MIT + file LICENSE MD5sum: 0321c11d833a1e6f7b28b563e3ff5835 Package: CSAR Version: 1.59.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: 6bed78d1ab9eeb4493386fcedd53876e Package: csaw Version: 1.41.1 Depends: R (>= 3.5.0), GenomicRanges, SummarizedExperiment Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod, utils LinkingTo: Rhtslib, Rcpp Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: 2a90052e3546f9662ca22b3d593d71cf Package: csdR Version: 1.13.3 Depends: R (>= 4.1.0) Imports: WGCNA, glue, RhpcBLASctl, 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ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), InteractiveComplexHeatmap License: Artistic-2.0 MD5sum: d570af75e2e520fdfe9c30d3c0de8290 Package: cTRAP Version: 1.25.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes License: MIT + file LICENSE MD5sum: 0770443b545c6367be0aad45a2e0dd85 Package: ctsGE Version: 1.33.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: 5ae2a79dfcb956ee72eba30d4d120e9a 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stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: 7f6c3aba18e335569f40ab915fb09f2b Package: CytoMDS Version: 1.3.5 Depends: R (>= 4.4), Biobase Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 MD5sum: 406de96fb4541426616afb25cd148142 Package: cytoMEM Version: 1.11.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: c503c50f843511f8530c3654a67ae05b Package: CytoML Version: 2.19.1 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>= 4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats, tibble LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel License_restricts_use: no MD5sum: 95fac25efdc7e3b519d8a3ccba7becb8 Package: CytoPipeline Version: 1.7.0 Depends: R (>= 4.4) Imports: methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1), ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI, diagram, jsonlite, scales Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, reshape2, dplyr, CytoPipelineGUI License: GPL-3 MD5sum: a4165f41417724c8f7ec4af4590b5d79 Package: CytoPipelineGUI Version: 1.5.0 Depends: R (>= 4.4), CytoPipeline Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 MD5sum: 2a92ea96c4f3782804ac1756d7b3b10d Package: 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rmarkdown, testthat License: GPL (>= 2) MD5sum: 10bca5857b6cf45e6816a3a62eb10a0a Package: daMA Version: 1.79.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 045bd7542767c7a6178fce41c4c093b8 Package: Damsel Version: 1.3.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils Suggests: BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene License: MIT + file LICENSE MD5sum: 5a4dc4fc97a11b4d74e7e028b3715b4f Package: DAPAR Version: 1.39.0 Depends: R (>= 4.3.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter, foreach Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db License: Artistic-2.0 MD5sum: f1bff047ea5c9d715c0ecfe8bf7dbb73 Package: DART Version: 1.55.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: aed717a9a860e8203f9e1a63012d1eef Package: dcanr Version: 1.23.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 743fa60562624497b4febb9227598af2 Package: DCATS Version: 1.5.0 Depends: R (>= 4.1.0), stats Imports: MCMCpack, matrixStats, robustbase, aod, e1071 Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: a296b03a2ec1944e5056929a0690470c Package: dcGSA Version: 1.35.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 59c7a2d14c195f3c2794403253f46b51 Package: ddCt Version: 1.63.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: testthat (>= 3.0.0), RUnit License: LGPL-3 MD5sum: c7287741b143035766aa2b0fdec075f0 Package: ddPCRclust Version: 1.27.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 MD5sum: 052095cab60a2bda9228ffc2938c6a78 Package: dearseq Version: 1.19.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, scattermore, stats, statmod, survey, tibble, viridisLite Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: 1596c8eee470f9d70d87624b6e70f331 Package: debCAM Version: 1.25.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: 970e777caf859a8b80cd2726c4e5aad8 Package: DECIPHER Version: 3.3.2 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), stats Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector Suggests: RSQLite (>= 1.1) License: GPL-3 MD5sum: 6a279efceb039743752e9e75f9e31be5 Package: DeconRNASeq Version: 1.49.0 Depends: R (>= 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methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: cdfe94a9afbc4862ea317e809520b93a Package: DifferentialRegulation Version: 2.5.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2, tximport, gridExtra LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 66f790e4d378ce88823f55ecd829dc59 Package: diffGeneAnalysis Version: 1.89.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL MD5sum: 57cdce936b38778e4b2f0492d988e423 Package: DiffLogo Version: 2.31.0 Depends: R (>= 3.4), stats, cba Imports: grDevices, graphics, utils, tools Suggests: knitr, testthat, seqLogo, MotifDb License: GPL (>= 2) MD5sum: 9f9f73d3e9c77d1baa5e22288f691a04 Package: diffuStats Version: 1.27.0 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VennDiagram, UpSetR, heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2 Suggests: testthat License: GPL-3 MD5sum: dc2950a2b2b0b228091ab222a38b3066 Package: distinct Version: 1.19.0 Depends: R (>= 4.3) Imports: Rcpp, stats, SummarizedExperiment, SingleCellExperiment, methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2, limma, scater LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle License: GPL (>= 3) MD5sum: ba6c3171bbbd482b0f093e8cd71521f0 Package: dittoSeq Version: 1.19.0 Depends: ggplot2 Imports: methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran License: MIT + file LICENSE MD5sum: adcd25caf866e972aef2d15bb939fef3 Package: divergence Version: 1.23.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 70de5ec2e1beefb5cb1d1ee2dc8cc22f Package: dks Version: 1.53.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: 75b65c0403dd9a234a26c9c759127b56 Package: DMRcaller Version: 1.39.0 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10) Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 31d64a75638311ef911218262237d005 Package: DMRcate Version: 3.3.1 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest License: file LICENSE MD5sum: 7a55353aee53cdae7ff73b200fbb7544 Package: DNABarcodeCompatibility Version: 1.23.0 Depends: R (>= 3.6.0) Imports: dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods, Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: file LICENSE MD5sum: 49cd6d193ecd5acdb52c4eee2a7398f1 Package: DNABarcodes Version: 1.37.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: 64b118cf99601f9778422dbddc99607d Package: DNAcopy Version: 1.81.0 License: GPL (>= 2) MD5sum: 6a3564ccbccbdb96cf1bb72d1d254dd1 Package: DNAfusion Version: 1.9.0 Depends: R (>= 4.2.0) Imports: bamsignals, GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle License: GPL-3 MD5sum: 5b029bb4e06a27954a3433358be07b8c Package: DNAshapeR Version: 1.35.0 Depends: R (>= 3.4), GenomicRanges Imports: Rcpp (>= 0.12.1), Biostrings, fields LinkingTo: Rcpp Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 MD5sum: 55eb01829a304dd2ceb34784f45dce05 Package: dominoSignal Version: 1.1.0 Depends: R(>= 4.2.0), Imports: biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment License: GPL-3 | file LICENSE MD5sum: c42b1d2a4e551f3db4c9301f84b00e95 Package: doppelgangR Version: 1.35.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) MD5sum: ccc4d3fac2c6c70aebcfbf8387fce47d Package: Doscheda Version: 1.29.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: a704458679ed6b5b72f0bcb72d414e23 Package: DOSE Version: 4.1.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim (>= 2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils (>= 0.1.6) Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat License: Artistic-2.0 MD5sum: 8a5466a09f450d477b9594e84baf1e66 Package: doseR Version: 1.23.0 Depends: R (>= 3.6) Imports: edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: 794e7880ec08d6ad3d51f76c5041bc23 Package: drawProteins Version: 1.27.0 Depends: R (>= 4.0) Imports: ggplot2, httr, dplyr, readr, tidyr Suggests: covr, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 2b52418606cbc6d8b4621a8edcee372a Package: dreamlet Version: 1.5.0 Depends: R (>= 4.3.0), variancePartition (>= 1.33.11), SingleCellExperiment, ggplot2 Imports: edgeR, SummarizedExperiment, DelayedMatrixStats, sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr, GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52), ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges, irlba, limma, metafor, remaCor, broom, tidyr, rlang, BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools, reshape2, ggrepel, scattermore, Rcpp, lme4 (>= 1.1-33), MASS, Rdpack, utils, stats LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, muscData, scater, scuttle License: Artistic-2.0 MD5sum: ad5167d2587ca4c4ff0a0e5681cf36da Package: DRIMSeq Version: 1.35.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 2d54269f57d4677a511c8c33e2dc1c58 Package: DriverNet Version: 1.47.0 Depends: R (>= 2.10), methods License: GPL-3 MD5sum: 40129c154882c49a46e0958fcabee2b6 Package: DropletUtils Version: 1.27.2 Depends: SingleCellExperiment Imports: utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel, SparseArray (>= 1.5.18), DelayedArray (>= 0.31.9), DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle LinkingTo: Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles License: GPL-3 MD5sum: bea041792e26db3f01a537b8ef67f8f0 Package: drugTargetInteractions Version: 1.15.0 Depends: methods, R (>= 4.1) Imports: utils, RSQLite, UniProt.ws, biomaRt,ensembldb, BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 License: Artistic-2.0 MD5sum: 1da1486f3091cba92fffd4f342aabea5 Package: DSS Version: 2.55.0 Depends: R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel Imports: utils, graphics, stats, splines Suggests: BiocStyle, knitr, rmarkdown, edgeR License: GPL MD5sum: e47b25814f5dac94a01168ca90c6e603 Package: dStruct Version: 1.13.0 Depends: R (>= 4.1) Imports: zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors, rlang, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 4a959c777e1195710845883977624888 Package: DTA Version: 2.53.0 Depends: R 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easyreporting Version: 1.19.0 Depends: R (>= 3.5.0) Imports: rmarkdown, methods, tools, shiny, rlang Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod License: Artistic-2.0 MD5sum: 8a697a7b886b006ad787da3bf59d0da3 Package: easyRNASeq Version: 2.43.0 Imports: Biobase (>= 2.64.0), BiocFileCache (>= 2.12.0), BiocGenerics (>= 0.50.0), BiocParallel (>= 1.38.0), biomaRt (>= 2.60.1), Biostrings (>= 2.72.1), edgeR (>= 4.2.1), GenomeInfoDb (>= 1.40.1), genomeIntervals (>= 1.60.0), GenomicAlignments (>= 1.40.0), GenomicRanges (>= 1.56.1), SummarizedExperiment (>= 1.34.0), graphics, IRanges (>= 2.38.1), LSD (>= 4.1-0), methods, parallel, rappdirs (>= 0.3.3), Rsamtools (>= 2.20.0), S4Vectors (>= 0.42.1), ShortRead (>= 1.62.0), utils Suggests: BiocStyle (>= 2.32.1), BSgenome (>= 1.72.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.33) License: Artistic-2.0 MD5sum: 1e54c5e15c3281099d1826063e91ea34 Package: EBarrays Version: 2.71.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) MD5sum: 76ddbcc5f55b05e4ce67104cc3ef2807 Package: EBcoexpress Version: 1.51.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) MD5sum: 0218dfb5f4eb5f69e5a20d754780eedc Package: EBImage Version: 4.49.0 Depends: methods Imports: BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind, tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils, htmltools, htmlwidgets, RCurl Suggests: BiocStyle, digest, knitr, rmarkdown, shiny License: LGPL MD5sum: bc3c7e0f9e0cacbd596d25db820d5dce Package: EBSeq Version: 2.5.1 Depends: blockmodeling, gplots, testthat, R (>= 3.0.0) Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0) LinkingTo: Rcpp,RcppEigen,BH License: Artistic-2.0 MD5sum: b6ddce56dc709e39c21a4bf67ae70ee1 Package: ecolitk Version: 1.79.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) MD5sum: a7eaed761e0568727d759d1f183475c0 Package: EDASeq Version: 2.41.0 Depends: Biobase (>= 2.15.1), ShortRead (>= 1.11.42) Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown License: Artistic-2.0 MD5sum: 646c9a4fa5fb7de3f678c1e87950fe03 Package: edge Version: 2.39.0 Depends: R(>= 3.1.0), Biobase Imports: methods, splines, sva, qvalue(>= 1.99.0), MASS Suggests: testthat, knitr, ggplot2, reshape2 License: MIT + file LICENSE MD5sum: 9d71c79cf4bf9a10e368edf538e800cd Package: edgeR Version: 4.5.1 Depends: R (>= 3.6.0), limma (>= 3.61.9) Imports: methods, graphics, stats, utils, locfit Suggests: jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject License: GPL (>= 2) MD5sum: d107fbebd5099f419d7724fc089ab0ce Package: EDIRquery Version: 1.7.0 Depends: R (>= 4.2.0) Imports: tibble (>= 3.1.6), tictoc (>= 1.0.1), utils (>= 4.1.3), stats (>= 4.1.3), readr (>= 2.1.2), InteractionSet (>= 1.22.0), GenomicRanges (>= 1.46.1) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: cef3eeef7ee94e01e530fa35d54f2d29 Package: eds Version: 1.9.0 Depends: Matrix Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, tximportData, testthat (>= 3.0.0) License: GPL-2 MD5sum: 94f939336469c424a843347b705511c1 Package: EGAD Version: 1.35.0 Depends: R(>= 3.5) Imports: gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo, igraph, plyr, MASS, RCurl, methods Suggests: knitr, testthat, rmarkdown, markdown License: GPL-2 MD5sum: 4bda4a40934db7de58afb6ac4d6c000a Package: EGSEA Version: 1.35.0 Depends: R (>= 4.3.0), Biobase, gage (>= 2.14.4), AnnotationDbi, topGO (>= 2.16.0), pathview (>= 1.4.2) Imports: PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0), limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1), htmlwidgets, plotly, DT Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: e972406d581417d1005364c05e1b9805 Package: eisaR Version: 1.19.0 Depends: R (>= 4.1) Imports: graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker, rtracklayer License: GPL-3 MD5sum: 4878511830c3e45468212c5f103dad38 Package: EMDomics Version: 2.37.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: 30509254caf6b483a8bafc54c78904ef Package: EmpiricalBrownsMethod Version: 1.35.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4b355737ad2af58f172763f476995dc2 Package: EnMCB Version: 1.19.0 Depends: R (>= 4.0) Imports: survivalROC, glmnet, rms, mboost, Matrix, igraph, methods, survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown License: GPL-2 MD5sum: 299eab3f1bf48807fa78cd0ceec52dd3 Package: ENmix Version: 1.43.2 Depends: parallel,doParallel,foreach,SummarizedExperiment,stats,R (>= 3.5.0) Imports: grDevices,graphics,matrixStats,methods,utils,irlba, geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut,IRanges,gtools, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 73a91fc1d5b727f7d7cb9a890c0b7a51 Package: EnrichDO Version: 1.1.1 Depends: R (>= 4.0.0) Imports: BiocGenerics, Rgraphviz, clusterProfiler, hash, S4Vectors, dplyr, ggplot2, graph, magrittr, methods, pheatmap, graphics, utils, purrr, tidyr, stats Suggests: knitr, rmarkdown, org.Hs.eg.db, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: 5c9a630459b0b821f550051cdd68bd07 Package: EnrichedHeatmap Version: 1.37.0 Depends: R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: 8096043fa2c25732e5d9a85df55e8bcc Package: EnrichmentBrowser Version: 2.37.0 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod License: Artistic-2.0 MD5sum: ac91bd0e9789d0e6599e6ec5f5bb58aa Package: enrichplot Version: 1.27.4 Depends: R (>= 3.5.0) Imports: aplot (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7), ggnewscale, ggplot2, ggrepel (>= 0.9.0), ggtangle (>= 0.0.5), graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, GOSemSim (>= 2.31.2), magrittr, ggtree, yulab.utils (>= 0.1.6) Suggests: clusterProfiler, dplyr, europepmc, ggarchery, ggupset, glue, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: 31c0fe1aaca8eec0593a65c4908ae754 Package: enrichViewNet Version: 1.5.0 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2, testthat, magick License: Artistic-2.0 MD5sum: 204eb8edae2e6a4c5b2a5d5a3868f936 Package: epialleleR Version: 1.15.1 Depends: R (>= 4.1) Imports: stats, methods, utils, data.table, BiocGenerics, GenomicRanges, Rcpp LinkingTo: Rcpp, BH, Rhtslib Suggests: GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 License: Artistic-2.0 MD5sum: 8a4ea435b21eae7158c2cfc3590532cd Package: EpiDISH Version: 2.23.1 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: e95883d2cf6d3ac7ef4cf3655326006b Package: epigenomix Version: 1.47.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: 9abba3882824f49bd9f742e7c7a3edab Package: EpiMix Version: 1.9.0 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 MD5sum: 6bd9faf9c40e55c3491275417c615ff5 Package: epiNEM Version: 1.31.0 Depends: R (>= 4.1) Imports: BoutrosLab.plotting.general, BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle License: GPL-3 MD5sum: 564c80e87d75844d9fa2527d737dfd70 Package: EpipwR Version: 1.1.0 Depends: R (>= 4.4.0) Imports: EpipwR.data, ExperimentHub (>= 2.10.0), ggplot2 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo License: Artistic-2.0 MD5sum: bc39696791194145ff9d22dadd26becc Package: epistack Version: 1.13.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: 9fcb1a66f5aa256f1dd0ce79f7653d1a Package: epistasisGA Version: 1.9.0 Depends: R (>= 4.2) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils LinkingTo: Rcpp, RcppArmadillo, BH, bigmemory Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 MD5sum: 7718862887e5ea3d0af2c0333f3c478a Package: EpiTxDb Version: 1.19.0 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: a3ca76b9d5ee39cc42142f02021c72b8 Package: epivizr Version: 2.37.0 Depends: R (>= 3.5.0), methods Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 MD5sum: 6e895783711972435edfd23cc0b92eff Package: epivizrChart Version: 1.29.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: 9a4d1681ff0fa4eb4990b4197dcbea65 Package: epivizrData Version: 1.35.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: 51c86d41e42ee4abc2888fc8b09fdaf8 Package: epivizrServer Version: 1.35.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: fdda3903fab538b064a65b2d93469756 Package: epivizrStandalone Version: 1.35.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, GenomeInfoDb, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: c13175b3ecdde3a25714d25ffaa06eb7 Package: erccdashboard Version: 1.41.0 Depends: R (>= 4.0), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr, knitr Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 0795c95cf55258ee4d4ddcafcf0861e2 Package: escape Version: 2.3.0 Depends: R (>= 4.1) Imports: AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject, Matrix Suggests: Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: 5c1d785d5417e6bac311883713922b4b Package: escheR Version: 1.7.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE MD5sum: b9e5765cc9e5c2e0dd2f627a65489427 Package: esetVis Version: 1.33.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 MD5sum: 12e3f48853709c2328316c5407992a9b Package: eudysbiome Version: 1.37.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: 534873963c4abe77893783324ed792ec Package: evaluomeR Version: 1.23.0 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0) Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: 2759caf4737139a5a2200c4bcda45b4a Package: EventPointer Version: 3.15.0 Depends: R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 MD5sum: fb7fa9120ff2e70a4f09d0f503db8890 Package: EWCE Version: 1.15.0 Depends: R (>= 4.2), RNOmni (>= 1.0) Imports: stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene (>= 0.99.8), data.table Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork License: GPL-3 MD5sum: 2164a052e13350eeb180a70cf82b37a2 Package: ExiMiR Version: 2.49.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) Suggests: mirna10cdf License: GPL-2 MD5sum: f4eb91427d03e8aec95de35355a31e38 Package: ExperimentHub Version: 2.15.0 Depends: methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.3.6), BiocFileCache (>= 1.5.1) Imports: utils, S4Vectors, BiocManager, rappdirs Suggests: knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments Enhances: ExperimentHubData License: Artistic-2.0 MD5sum: 11b97b333e23ea631c36d5666198e677 Package: ExperimentHubData Version: 1.33.0 Depends: utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData (>= 1.21.3) Imports: methods, ExperimentHub, BiocManager, DBI, httr, curl Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 34ad7c1e836d1e8ba113a794015e3fb6 Package: ExperimentSubset Version: 1.17.0 Depends: R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment, SpatialExperiment, TreeSummarizedExperiment Imports: methods, Matrix, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway License: MIT + file LICENSE MD5sum: 8eb4c3113e53b3bb27f1bd59d97baea7 Package: ExploreModelMatrix Version: 1.19.2 Imports: shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr, magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS, limma, S4Vectors, shinyjs Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle License: MIT + file LICENSE MD5sum: cc87ecee712054cbcb7712d7da360660 Package: ExpressionAtlas Version: 1.35.0 Depends: R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 12647c1deaa907fb25ccf32660b81c69 Package: fabia Version: 2.53.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils 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ontologyIndex, tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT, clusterProfiler, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager License: GPL-3 MD5sum: ff00029ce0718e9b2eb013af78574475 Package: fastLiquidAssociation Version: 1.43.0 Depends: methods, LiquidAssociation, parallel, doParallel, stats, Hmisc, utils Imports: WGCNA, impute, preprocessCore Suggests: GOstats, yeastCC, org.Sc.sgd.db License: GPL-2 MD5sum: da53cd89260267ce08f34fef99a6c658 Package: FastqCleaner Version: 1.25.0 Imports: methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d46c1c137e2562f4ac63c77d36f5abdb Package: fastreeR Version: 1.11.0 Depends: R (>= 4.4) Imports: ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils Suggests: BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, 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RColorBrewer, png, methods, stats, utils, graphics, grDevices Suggests: RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager License: GPL (>= 2) MD5sum: 8bbf7934fd9a34d1ff14f2145f676e91 Package: fgsea Version: 1.33.2 Depends: R (>= 4.1) Imports: Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), cowplot, grid, fastmatch, Matrix, scales, utils LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat License: MIT + file LICENCE MD5sum: 57db5a360275aa18565bd62748f6b80e Package: FilterFFPE Version: 1.17.0 Imports: foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors Suggests: BiocStyle License: LGPL-3 MD5sum: 46b3a93422c6237c568d41c11558bc9d Package: findIPs Version: 1.3.1 Depends: graphics, R (>= 4.4.0) Imports: Biobase, BiocParallel, parallel, stats, SummarizedExperiment, survival, utils 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GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 506fd24e65cf300a216cecfdf2d4f048 Package: GeneSelectMMD Version: 2.51.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: ee1be049648168a980e86af2e6a76cc5 Package: GENESIS Version: 2.37.0 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 5280377b3a25992b62dacdee00b24a5c Package: geNetClassifier Version: 1.47.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 4268711701c985f59b7b67f3dff6b9b5 Package: GENIE3 Version: 1.29.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: 6ab4c00c85679405a83c8104cc6b133b Package: GenomAutomorphism Version: 1.9.1 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb, GenomicRanges, IRanges, matrixStats, XVector, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 MD5sum: 16b1023ce3195964ac2c4ba5317a6f57 Package: GenomeInfoDb Version: 1.43.3 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.41.1) Imports: stats, stats4, utils, UCSC.utils, GenomeInfoDbData Suggests: R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: ce8bade3065e2173ff62edb44f6e5f66 Package: genomeIntervals Version: 1.63.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: 09e138f891c972054f42e6f8b0d26062 Package: genomes Version: 3.37.0 Depends: readr, curl License: GPL-3 MD5sum: b35d445bc8cfc68d40b2e5879acdd8bd Package: GenomicAlignments Version: 1.43.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.55.3), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: 21372118aa4574d9f363e84c407e96ae Package: GenomicDataCommons Version: 1.31.0 Depends: R (>= 4.1.0) Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 MD5sum: df67b66833c54b76274b2a327a582d74 Package: GenomicDistributions Version: 1.15.0 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE MD5sum: d1c37e6d9aadc6f77da68b60e4718dc8 Package: genomicInstability Version: 1.13.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: 5212f187a0065844e938eaa1b73e0f82 Package: GenomicInteractionNodes Version: 1.11.1 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: 388644cf30fef60d08ef818d09104049 Package: GenomicOZone Version: 1.21.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 54c94654fa2986f74551cf47c3f13038 Package: GenomicRanges Version: 1.59.1 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.41.1), GenomeInfoDb (>= 1.43.1) Imports: utils, stats, XVector (>= 0.29.2) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: c2475f1a04dce0b6800a9791ab126f67 Package: GenomicScores Version: 2.19.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: b6f44161e4287be8393f3904709d04dd Package: GenomicSuperSignature Version: 1.15.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: db04a37ee29008470aacb4c55e6b706f Package: GenomicTuples Version: 1.41.1 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings License: Artistic-2.0 MD5sum: 4ea973a2d99117e4e49298d4c4779f6d Package: GeoDiff Version: 1.13.0 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 23079132eee52b7b12f9832b2daf8c1a Package: GEOfastq Version: 1.15.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 0c24fc87d7fff36df2173023dfb49b7a Package: GEOmetadb Version: 1.69.2 Depends: R.utils,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 5012d52daf46dc76f10a8fc986e6bc18 Package: geomeTriD Version: 1.1.7 Depends: R (>= 4.4.0) Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, rgl, rjson, S4Vectors, scales, stats, trackViewer Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 84212314e65bab20fb38925155fe1ab4 Package: GeomxTools Version: 3.11.0 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT MD5sum: 16c3e8e93f02e3c98f67350ae7b7dd56 Package: GEOquery Version: 2.75.0 Depends: methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, rentrez, R.utils, stringr, SummarizedExperiment, S4Vectors, rvest, httr2 Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown License: MIT + file LICENSE MD5sum: 90c79c16244be21d78df2360fcb35cf6 Package: GEOsubmission Version: 1.59.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: 248ad4a1b68282eb698d1268f67881b6 Package: GeoTcgaData Version: 2.7.0 Depends: R (>= 4.2.0) Imports: utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics License: Artistic-2.0 MD5sum: b7f6dfa50faa86b4d593f40e06ebc649 Package: gep2pep Version: 1.27.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 45378a8c71a66f9671271c32fc7f3341 Package: getDEE2 Version: 1.17.3 Depends: R (>= 4.0) Imports: stats, utils, SummarizedExperiment, htm2txt Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: 2005acecacd1b1f038a95e53ae2a92a2 Package: geva Version: 1.15.0 Depends: R (>= 4.1) Imports: grDevices, graphics, methods, stats, utils, dbscan, fastcluster, matrixStats Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) License: LGPL-3 MD5sum: c5dbf440b5731b332defddf299b5448d Package: GEWIST Version: 1.51.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: 3eea3d1d8137d5073eaa5c94b1b37cf1 Package: geyser Version: 0.99.8 Depends: R (>= 3.5.0) Imports: bslib (>= 0.6.0), BiocStyle, ComplexHeatmap, dplyr, DT, ggbeeswarm, ggplot2, htmltools, magrittr, shiny, SummarizedExperiment, tibble, tidyselect, tidyr Suggests: airway, knitr, DESeq2, recount3, rmarkdown, stringr, testthat (>= 3.0.0) License: CC0 MD5sum: 11749f80779ae688d1b13428fecd9364 Package: ggcyto Version: 1.35.0 Depends: methods, ggplot2(>= 3.5.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.3.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: file LICENSE MD5sum: d0b54399ea8867c8d7132fdf4aa3aa0b Package: ggkegg Version: 1.5.0 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, GetoptLong, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, methods, utils, stats, grDevices, gtable Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, AnnotationDbi, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ee305901c202e1698df5570b327b7550 Package: ggmanh Version: 1.11.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, paletteer, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats, tidyr, dplyr, pals, magrittr Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), GenomicRanges License: MIT + file LICENSE MD5sum: b50ff52d42d04213d859d03efbe93566 Package: ggmsa Version: 1.13.1 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, statebins, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 2c9b521d6f30a2e46e623e5e66a46ac9 Package: GGPA Version: 1.19.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 79a7132278e8b231d98dfc6fa4d04a75 Package: ggsc Version: 1.5.0 Imports: Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2, grDevices, grid, methods, rlang, scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, RColorBrewer, yulab.utils, scales LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS License: Artistic-2.0 MD5sum: 31f2e12063273ea4c7d40685348dd50f Package: ggseqalign Version: 1.1.0 Depends: R (>= 4.4.0) Imports: pwalign, dplyr, ggplot2 Suggests: Biostrings, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: aa0d0b6e02de184e291c433d62e232cf Package: ggspavis Version: 1.13.0 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE MD5sum: abcd37446227c1cf0119670327090da6 Package: ggtree Version: 3.15.0 Depends: R (>= 3.5.0) Imports: ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>= 0.1.6), tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats, cli Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue License: Artistic-2.0 MD5sum: f2ce1c7c825b9786564e345d8e8f271e Package: ggtreeDendro Version: 1.9.0 Depends: ggtree (>= 3.5.3) Imports: ggplot2, stats, tidytree, utils Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils License: Artistic-2.0 MD5sum: 19c5b65a6f2f1c5223c49387f7f3abb5 Package: ggtreeExtra Version: 1.17.0 Imports: ggplot2, utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli, magrittr Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar License: GPL (>= 3) MD5sum: 7e3a8194466a971d1417acfd5007adf6 Package: ggtreeSpace Version: 1.3.0 Imports: interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools, rlang, tibble, tidyr, tidyselect, stats Suggests: knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: a5e0300f8e0e9b6729cad23b3502df73 Package: GIGSEA Version: 1.25.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 05a452080270592de804b1c6323c61a9 Package: ginmappeR Version: 1.3.3 Imports: KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise, cachem, jsonlite, rvest Suggests: RUnit, BiocGenerics, markdown, knitr License: GPL-3 + file LICENSE MD5sum: 706e18cf87d4d7ba5c72adeb38b82066 Package: gINTomics Version: 1.3.0 Depends: R (>= 4.4.0) Imports: BiocParallel, biomaRt, OmnipathR, edgeR, ggplot2, ggridges, gtools, MultiAssayExperiment, plyr, stringi, stringr, SummarizedExperiment, methods, stats, reshape2, randomForest, limma, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics, GenomicFeatures, ReactomePA, clusterProfiler, dplyr, AnnotationDbi, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, shiny, GenomicRanges, ggtree, shinydashboard, plotly, DT, MASS, InteractiveComplexHeatmap, ComplexHeatmap, visNetwork, shiny.gosling, ggvenn, RColorBrewer, utils, grDevices, callr, circlize Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 699f2294747447d600138977fc0b7216 Package: GladiaTOX Version: 1.23.0 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 9f30c739305a88a979e26f9a0e1c2307 Package: glmGamPoi Version: 1.19.2 Imports: Rcpp, beachmat, DelayedMatrixStats, matrixStats, MatrixGenerics, SparseArray (>= 1.5.21), DelayedArray, HDF5Array, Matrix, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs LinkingTo: Rcpp, RcppArmadillo, beachmat, assorthead Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, MASS, statmod, ggplot2, bench, BiocParallel, knitr, 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ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 821802f17a5d5c062763a68e9d90fd42 Package: GNOSIS Version: 1.5.0 Depends: R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools Imports: DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: bf0693896c3acbb7ded1c2d31bc3d23e Package: GOexpress Version: 1.41.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: 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stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: 07e384bacc202db5108d375e98e24c2b Package: GSCA Version: 2.37.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: e619ad0726489c4fddc0a2a2f9694d53 Package: gscreend Version: 1.21.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: ce328b57429358f1335e770ab7b6bd5c Package: GSEABase Version: 1.69.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, 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LICENSE MD5sum: abdde1d9fb9fb5ac7fe397c7deb25186 Package: GSgalgoR Version: 1.17.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE MD5sum: d4f79e0639da703ca0dc37b2b2fe135d Package: GSReg Version: 1.41.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: 7e98b1629260a6f7664a2442ee1be388 Package: GSRI Version: 2.55.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: 5166170ecd5d40275ba78e74c59a4c2b Package: GSVA Version: 2.1.5 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, S4Vectors, IRanges, Biobase, 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parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: e296e7cdcbe3d426b14b1afb2ba65a88 Package: GWAS.BAYES Version: 1.17.0 Depends: R (>= 4.3.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), limma (>= 3.54.0), stats (>= 4.2.2), MASS (>= 7.3-58.1) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP License: GPL-3 + file LICENSE MD5sum: 3f078eac7ff2d3ced04ede70fc00ec40 Package: GWASTools Version: 1.53.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, 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IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks (>= 2.29.4) License: GPL-3 MD5sum: 0da3f187ea9d8e338b3b96711ea61aa7 Package: infercnv Version: 1.23.0 Depends: R(>= 4.0) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: be043b283139e2ec5172836dbde9d56f Package: infinityFlow Version: 1.17.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: 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RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase Enhances: rstudio License: Artistic-2.0 MD5sum: 3ca8f4335a46c8c18340053dd911f025 Package: interactiveDisplayBase Version: 1.45.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny, DT Suggests: knitr, markdown Enhances: rstudioapi License: Artistic-2.0 MD5sum: 4b6ff8a0c3b1eeeddd801d3c013bdaa4 Package: InterCellar Version: 2.13.0 Depends: R (>= 4.1) Imports: config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr License: MIT + 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readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, DT Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, data.table, Rcapture License: CC BY 4.0 MD5sum: caf27b0e0bcbc1c4a6a8f1f8a97f0a12 Package: iSEE Version: 2.19.2 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges License: MIT + file LICENSE MD5sum: 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SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: 906326b18f3dc2fe3eb4ce1f95ddee26 Package: KEGGgraph Version: 1.67.0 Depends: R (>= 3.5.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: b418378448205ef160028c65e79e41e1 Package: KEGGlincs Version: 1.33.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: 069c4492ce799a8837f54f3b807ce6b9 Package: keggorthology Version: 2.59.0 Depends: R (>= 2.5.0), hgu95av2.db, graph Imports: AnnotationDbi, DBI, grDevices, methods, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 MD5sum: 4899f1343dd33b1da07cb6739e041bc4 Package: KEGGREST Version: 1.47.0 Depends: R (>= 3.5.0) Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: e3b9d59935133fb76924e3c82528b0fe Package: KinSwingR Version: 1.25.0 Depends: R (>= 3.5) Imports: data.table, BiocParallel, sqldf, stats, grid, grDevices Suggests: knitr, rmarkdown License: GPL-3 MD5sum: a2a35293f2a4dcd8580c83655fcc96b7 Package: kmcut Version: 1.1.0 Imports: survival, tools, methods, pracma, doParallel, foreach, parallel, SummarizedExperiment, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, License: Artistic-2.0 MD5sum: d721bffaffaea2e43500ebe6eef844f5 Package: KnowSeq Version: 1.21.0 Depends: R (>= 4.0), cqn (>= 1.28.1) Imports: stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab, rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML, praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3), limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0), gridExtra Suggests: knitr License: GPL (>= 2) MD5sum: cad5bdfe898c3f9aef14ffd40b7a773e Package: knowYourCG Version: 1.3.15 Depends: R (>= 4.4.0) Imports: sesameData, dplyr, methods, rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats, stringr, utils, ggplot2, ggrepel, tibble, wheatmap, magrittr Suggests: testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr, sesame, gprofiler2, ggrastr License: MIT + file LICENSE MD5sum: 8d822478ab0b11fdfcf6f8e7cf1013a1 Package: koinar Version: 1.1.2 Depends: R (>= 4.3) Imports: httr, jsonlite, methods, utils Suggests: BiocManager, BiocStyle (>= 2.26), httptest, knitr, lattice, msdata, OrgMassSpecR, protViz, S4Vectors, Spectra, testthat, mzR License: Apache License 2.0 MD5sum: 762b2640a2c395c9d3d23ade5208a783 Package: LACE Version: 2.11.0 Depends: R (>= 4.2.0) Imports: curl, igraph, foreach, doParallel, sortable, dplyr, forcats, data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast, stats, SummarizedExperiment, utils, purrr, stringi, stringr, Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs, data.table, htmltools, htmlwidgets, bsplus, shinyvalidate, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr, logr, ggplot2, svglite Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown License: file LICENSE MD5sum: 893706c4990b02860be69be29fcafb8f Package: LBE Version: 1.75.0 Depends: stats Imports: graphics, stats, utils Suggests: qvalue License: GPL-2 MD5sum: 54b0063d42b8f9ced3a030cf739bb198 Package: ldblock Version: 1.37.0 Depends: R (>= 3.5), methods, rlang Imports: BiocGenerics (>= 0.25.1), httr, Matrix Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) License: Artistic-2.0 MD5sum: 4e2750d95ca437518eb9854c2caf222c Package: LedPred Version: 1.41.0 Depends: R (>= 3.2.0), e1071 (>= 1.6) Imports: akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat License: MIT | file LICENSE MD5sum: 58119c6107240417c9eb94c6e2f61176 Package: lefser Version: 1.17.3 Depends: SummarizedExperiment, R (>= 4.0.0) Imports: coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr, testthat, tibble, tidyr, forcats, stringr, ggtree, BiocGenerics, ape, ggrepel, mia, purrr, tidyselect, treeio Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, pkgdown, covr, withr License: Artistic-2.0 MD5sum: 09adce6ff644c1f9145b5854eb0bbe2f Package: lemur Version: 1.5.0 Depends: R (>= 4.1) Imports: stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang (>= 1.1.0), vctrs (>= 0.6.0), glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, harmony (>= 1.2.0), limma, BiocNeighbors LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: e2e6cc9803c83b42ce8ce7cf0e63e1c7 Package: les Version: 1.57.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 MD5sum: 6f9775f7b8fb413fdf5215909b6183e3 Package: levi Version: 1.25.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat, methods, rmarkdown LinkingTo: Rcpp Suggests: rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: f9cd7a9e03900199954af1559d852547 Package: lfa Version: 2.7.0 Depends: R (>= 4.0) Imports: utils, methods, corpcor, RSpectra Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: 1d4451430c5cbd3c360289076326fb94 Package: limma Version: 3.63.3 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods, statmod Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn License: GPL (>= 2) MD5sum: d293344948adc318b9208d0a7c12d07e Package: limmaGUI Version: 1.83.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) MD5sum: 26c04d37142e57ad01765c86f7702e54 Package: limpca Version: 1.3.0 Depends: R (>= 3.5.0) Imports: ggplot2, stringr, plyr, ggrepel, reshape2, grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 220a9255361b212e958528b2ccdf57c5 Package: LimROTS Version: 0.99.12 Depends: R (>= 4.5.0), SummarizedExperiment Imports: limma, stringr, qvalue, utils, stats, BiocParallel, basilisk.utils, S4Vectors, dplyr Suggests: BiocStyle, ggplot2, magick, testthat (>= 3.0.0), knitr, rmarkdown, caret, ROTS License: Artistic-2.0 MD5sum: 161e075d582e3f39221dca361430ea58 Package: LinkHD Version: 1.21.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: dd42fb695315f20a7a88072a9437c045 Package: Linnorm Version: 2.31.0 Depends: R(>= 4.1.0) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats License: MIT + file LICENSE MD5sum: 2c9f9f96e5fbc350bf6be3e61be51b11 Package: LinTInd Version: 1.11.0 Depends: R (>= 4.0), ggplot2, parallel, stats, S4Vectors Imports: data.tree, reshape2, networkD3, stringdist, purrr, ape, cowplot, ggnewscale, stringr, dplyr, rlist, pheatmap, Biostrings, pwalign, IRanges, BiocGenerics(>= 0.36.1), ggtree Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 403c953699bec031bef8823ce0a0a415 Package: lionessR Version: 1.21.0 Depends: R (>= 3.6.0) Imports: stats, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, igraph, reshape2, limma, License: MIT + file LICENSE MD5sum: 7210350198f63878677b5d8b943d2261 Package: lipidr Version: 2.21.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat License: MIT + file LICENSE MD5sum: 4f27671714ca40a0cce868247f3246d9 Package: LiquidAssociation Version: 1.61.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: d9ff205d266855ec5dd4c24990402296 Package: lisaClust Version: 1.15.6 Depends: R (>= 4.0) Imports: ggplot2, class, concaveman, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap, spatstat.random, lifecycle, simpleSeg, rlang, Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: c5b705c145cd05c16014134f7c5c6c47 Package: lmdme Version: 1.49.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) MD5sum: 2197d21f910e7dac1cba1feab3a9577e Package: loci2path Version: 1.27.0 Depends: R (>= 3.5.0) Imports: pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: c41e4366ac746316494e6a73ec3c8a7e Package: logicFS Version: 2.27.0 Depends: LogicReg, mcbiopi, survival Imports: graphics, methods, stats Suggests: genefilter, siggenes License: LGPL (>= 2) MD5sum: fbca61990ea714397192a3b4bc53d916 Package: LOLA Version: 1.37.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown Enhances: simpleCache, qvalue, ggplot2 License: GPL-3 MD5sum: 8dbb9ad54eb1156898a028178d6facd4 Package: LoomExperiment Version: 1.25.0 Depends: R (>= 3.5.0), S4Vectors, SingleCellExperiment, SummarizedExperiment, methods, rhdf5, BiocIO Imports: DelayedArray, GenomicRanges, HDF5Array, Matrix, stats, stringr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate License: Artistic-2.0 MD5sum: 278ee26207105041adbfc7f1ace1528e Package: LPE Version: 1.81.0 Depends: R (>= 2.10) Imports: stats License: LGPL MD5sum: a0c2032a947ebadbb9d5b0eb843f57c7 Package: lpNet Version: 2.39.0 Depends: lpSolve, KEGGgraph License: Artistic License 2.0 MD5sum: 5661ad356cbae5749435df2fdfb38558 Package: lpsymphony Version: 1.35.0 Depends: R (>= 3.0.0) Suggests: BiocStyle, knitr, testthat Enhances: slam License: EPL MD5sum: c1aa4be89bce205d2657a5b48fac8496 Package: LRBaseDbi Version: 2.17.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase Suggests: testthat, BiocStyle, AnnotationHub License: Artistic-2.0 MD5sum: 2bf4492755b056044ed89c374b37bfb9 Package: LRcell Version: 1.15.0 Depends: R (>= 4.1), ExperimentHub, AnnotationHub Imports: BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils Suggests: LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: 974540a1bc58b741023bc43a783b066a Package: lumi Version: 2.59.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) MD5sum: cded8d60cbd35d53b6d0b218e4c28a9c Package: LymphoSeq Version: 1.35.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 MD5sum: 835669cb0792046291557c322366fa25 Package: M3C Version: 1.29.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, cluster, parallel, foreach, doParallel, matrixcalc, Rtsne, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 MD5sum: d4291edb1aeeece56708091a8fab6afc Package: M3Drop Version: 1.33.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods, scater Suggests: ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase License: GPL (>= 2) MD5sum: 698a6a14d7bd7116652e2ddd2706686b Package: Maaslin2 Version: 1.21.0 Depends: R (>= 3.6) Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4, tibble Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE MD5sum: dcd3d34cd4ece662b8c116f466bbfaae Package: maaslin3 Version: 0.99.3 Depends: R (>= 4.4) Imports: dplyr, pbapply, lmerTest, parallel, lme4, optparse, logging, multcomp, ggplot2, RColorBrewer, patchwork, scales, rlang, tibble, ggnewscale, survival, methods, BiocGenerics, SummarizedExperiment, TreeSummarizedExperiment Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra License: MIT + file LICENSE MD5sum: 9d4448e0614577111d87d41fbf7a0007 Package: Macarron Version: 1.11.0 Depends: R (>= 4.2.0), SummarizedExperiment Imports: BiocParallel, DelayedArray, WGCNA, ff, data.table, dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, httr, RJSONIO, logging, methods, utils Suggests: knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE MD5sum: 9dda4988400a5736b50d0430f85d6828 Package: maCorrPlot Version: 1.77.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) MD5sum: ec48eab355787a5ee393da2b3bcf21d8 Package: MACSQuantifyR Version: 1.21.0 Imports: readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel, methods, stats, latticeExtra, lattice, rmarkdown, png, grid, gridExtra, prettydoc, rvest, xml2 Suggests: knitr, testthat, R.utils, spelling License: Artistic-2.0 MD5sum: cf17309d782c569a76a8d80745901819 Package: MACSr Version: 1.15.0 Depends: R (>= 4.1.0) Imports: utils, reticulate, S4Vectors, methods, basilisk, ExperimentHub, AnnotationHub Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata License: BSD_3_clause + file LICENSE MD5sum: b82f58efc9cbe24802f869149bf55adb Package: made4 Version: 1.81.0 Depends: RColorBrewer,gplots,scatterplot3d, Biobase, SummarizedExperiment Imports: ade4 Suggests: affy, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: e07076b5245f277adfb8e44e5f2a3720 Package: maftools Version: 2.23.0 Depends: R (>= 3.3) Imports: data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy, pheatmap LinkingTo: Rhtslib, zlibbioc Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, curl License: MIT + file LICENSE MD5sum: 2c45024e1fb6782817d34195af794abc Package: magrene Version: 1.9.0 Depends: R (>= 4.2.0) Imports: utils, stats, BiocParallel Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: 40d01933adade05c857ec86e04a27880 Package: MAI Version: 1.13.0 Depends: R (>= 3.5.0) Imports: caret, parallel, doParallel, foreach, e1071, future.apply, future, missForest, pcaMethods, tidyverse, stats, utils, methods, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1e490ce63c48dd7a6f071b40408d6518 Package: makecdfenv Version: 1.83.1 Depends: R (>= 2.6.0), affyio Imports: Biobase, affy, methods, stats, utils License: GPL (>= 2) MD5sum: d018107c327e11769b6cb59521e7bdd9 Package: MantelCorr Version: 1.77.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) MD5sum: 5f1d35043bc4f12013a4f8d730dd0b20 Package: MAPFX Version: 1.3.0 Depends: R (>= 4.4.0) Imports: flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2, RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils, e1071, xgboost, parallel, pbapply, reshape2, gtools, utils, stats, cowplot, methods, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 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marinerData License: GPL-3 MD5sum: 8cd2eecca6a2f58e468665cbc29644a5 Package: marr Version: 1.17.0 Depends: R (>= 4.0) Imports: Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, covr License: GPL (>= 3) MD5sum: fbf6b1e558459af2b8548697d5bf4343 Package: marray Version: 1.85.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL MD5sum: 174b1d27ed5cd4aff6d93ba709669e5d Package: martini Version: 1.27.0 Depends: R (>= 4.0) Imports: igraph (>= 1.0.1), Matrix, memoise (>= 2.0.0), methods (>= 3.3.2), Rcpp (>= 0.12.8), snpStats (>= 1.20.0), stats, utils, LinkingTo: Rcpp, RcppEigen (>= 0.3.3.5.0) Suggests: biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>= 2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>= 0.12.2), knitr, testthat, readr, rmarkdown License: GPL-3 MD5sum: a5a163cf8825cc418cf969926db6272d Package: maSigPro Version: 1.79.0 Depends: R (>= 2.3.1) Imports: Biobase, graphics, grDevices, venn, mclust, stats, MASS License: GPL (>= 2) MD5sum: 505e094c079830613493ccd1c13c1b26 Package: maskBAD Version: 1.51.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe, hgu95av2cdf License: GPL (>= 2) MD5sum: 8e56727cac33ef7c483851ac737f49f7 Package: MassArray Version: 1.59.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: 91df46e6a12d1065adf3f434ad55a482 Package: massiR Version: 1.43.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 MD5sum: 955f7c2baaf6ab50fb2333b21102377d Package: MassSpecWavelet Version: 1.73.1 Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench License: LGPL (>= 2) MD5sum: 9149337c61e6d3b3c124913603417c6f Package: mastR Version: 1.7.0 Depends: R (>= 4.3.0) Imports: AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr, graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb, org.Hs.eg.db, patchwork, SeuratObject, SingleCellExperiment, stats, SummarizedExperiment, tidyr, utils Suggests: BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR License: MIT + file LICENSE MD5sum: 1c13d6e27476eadcb4edbec9586539f4 Package: matchBox Version: 1.49.0 Depends: R (>= 2.8.0) License: Artistic-2.0 MD5sum: 4c5312a42ebfc13aee05ba91a8ce6ec6 Package: MatrixGenerics Version: 1.19.1 Depends: matrixStats (>= 1.4.1) Imports: methods Suggests: Matrix, sparseMatrixStats, SparseArray, DelayedArray, DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: eb57ee4ba227862f5da15a6c62961142 Package: MatrixQCvis Version: 1.15.0 Depends: DT (>= 0.33), SummarizedExperiment (>= 1.20.0), plotly (>= 4.9.3), shiny (>= 1.6.0) Imports: ComplexHeatmap (>= 2.7.9), dplyr (>= 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Artistic-2.0 | file LICENSE MD5sum: ff0e38733a82a2cfa8e1b705fc9a502d Package: MBAmethyl Version: 1.41.0 Depends: R (>= 2.15) License: Artistic-2.0 MD5sum: 1ba339c42aaa6a4b7d84de58c22f1978 Package: MBASED Version: 1.41.0 Depends: RUnit, BiocGenerics, BiocParallel, GenomicRanges, SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 9c4efa23839cd953c66c2f65cd9b482f Package: MBCB Version: 1.61.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) MD5sum: 1aa4c64689960e7c186481de3a5c4c2d Package: mbkmeans Version: 1.23.0 Depends: R (>= 3.6) Imports: methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix, BiocParallel LinkingTo: Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: 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magrittr Suggests: covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat License: Artistic-2.0 MD5sum: ba65eb059306df3f2e0872679b691f84 Package: MEIGOR Version: 1.41.0 Depends: R (>= 4.0), Rsolnp, snowfall, deSolve, CNORode Suggests: CellNOptR, knitr, BiocStyle License: GPL-3 MD5sum: 42ef0a9c98c51653e603dd2d09244ce2 Package: Melissa Version: 1.23.0 Depends: R (>= 3.5.0), BPRMeth, GenomicRanges Imports: data.table, parallel, ROCR, matrixcalc, mclust, ggplot2, doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm, truncnorm, assertthat, BiocStyle, stats, utils Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 89a8a3c465ddd721bd4bfcd710d7d833 Package: memes Version: 1.15.0 Depends: R (>= 4.1) Imports: Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2, ggseqlogo, magrittr, matrixStats, methods, patchwork, processx, purrr, rlang, readr, stats, tools, tibble, tidyr, utils, usethis, universalmotif (>= 1.9.3), xml2 Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr License: MIT + file LICENSE MD5sum: e1f1f9b9b79935d1585224771f6bbb28 Package: Mergeomics Version: 1.35.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 6f839b8744245629e18e79618d93d157 Package: MeSHDbi Version: 1.43.0 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: testthat License: Artistic-2.0 MD5sum: a4c665a42dccfcf89b69b19faac2e026 Package: meshes Version: 1.33.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, DOSE, enrichplot, GOSemSim (>= 2.31.2), methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5) Suggests: knitr, rmarkdown, prettydoc License: Artistic-2.0 MD5sum: ae5e7193ec12f02014b293f3c927ed0d Package: meshr Version: 2.13.0 Depends: R (>= 4.1.0) Imports: markdown, 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Artistic-2.0 MD5sum: c07dc9dae7939f9e0c2e9edf47c1ff03 Package: MetaboCoreUtils Version: 1.15.0 Depends: R (>= 4.0) Imports: utils, MsCoreUtils, BiocParallel, methods, stats Suggests: BiocStyle, testthat, knitr, rmarkdown, robustbase License: Artistic-2.0 MD5sum: 0f7438aa8ecdd69152c8503f6b4cc3f8 Package: metabolomicsWorkbenchR Version: 1.17.0 Depends: R (>= 4.0) Imports: data.table, httr, jsonlite, methods, MultiAssayExperiment, struct, SummarizedExperiment, utils Suggests: BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown, structToolbox, testthat, pmp, grid, png License: GPL-3 MD5sum: 5e3809fc7847a6b10851486c2c6c14d1 Package: metabomxtr Version: 1.41.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 MD5sum: cbcad577dd61f3101ff0447278776fdd Package: MetaboSignal Version: 1.37.0 Depends: R(>= 3.3) Imports: KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 81f2bf01e9883776f19e747d208c1ce0 Package: metaCCA Version: 1.35.0 Suggests: knitr License: MIT + file LICENSE MD5sum: 054154023310c83f4ef3a40ac45c5a24 Package: MetaCyto Version: 1.29.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr, rmarkdown License: GPL (>= 2) MD5sum: 01d1f9d84d4da06ce650fd7ca4ed5715 Package: metagenomeSeq Version: 1.49.1 Depends: R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer Imports: parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 MD5sum: 8cfffe77dea6e157ed2a8106fde6040d Package: metahdep Version: 1.65.0 Depends: R (>= 2.10), methods 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metapone Version: 1.13.0 Depends: R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel Imports: methods Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: af765c791ac0c2ae11b3372c9166a5d6 Package: metaSeq Version: 1.47.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: 738a41300a7c215e0f85ea7438f3d41c Package: MetCirc Version: 1.37.0 Depends: R (>= 4.4), amap (>= 0.8), circlize (>= 0.4.16), scales (>= 1.3.0), shiny (>= 1.8.1.1), Spectra (>= 1.15.3) Imports: ggplot2 (>= 3.5.1), MsCoreUtils (>= 1.17.0), S4Vectors (>= 0.43.1) Suggests: BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1) License: GPL (>= 3) MD5sum: 097a63b031a9dd3ce1ba0a54509497cf Package: methimpute Version: 1.29.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 4ed27924e23c2be676a196c68bb07d32 Package: MethPed Version: 1.35.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 7b1846f99a39ec31caa767d1e2e481f7 Package: MethTargetedNGS Version: 1.39.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: be6a96bdb065e1c448d71a73e92126d0 Package: MethylAid Version: 1.41.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: eb79c94f988c873cf8c2a2351a795844 Package: methylCC Version: 1.21.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: 73f18591f4dd153031b581b965087b9d Package: methylclock Version: 1.13.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE MD5sum: acab78cf80418085055c51981a87d7ba Package: methylGSA Version: 1.25.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: 8576dbb760206a0e99d0cda85cbe44a8 Package: methyLImp2 Version: 1.3.0 Depends: R (>= 4.3.0), ChAMPdata Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 787834f62fcea0e8b7d949f16eb50032 Package: MethylMix Version: 2.37.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 961e3498335e3ebe45a823ddd2fb40c6 Package: methylMnM Version: 1.45.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 87be4cf2291e7f6d9e99f2a3d4c77573 Package: methylPipe Version: 1.41.0 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: 2f2ca4faf0038ddea6595e49975d4a10 Package: methylscaper Version: 1.15.0 Depends: R (>= 4.4.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils License: GPL-2 MD5sum: bc4ce46c4ec571a77f9722dcac898e31 Package: methylSig Version: 1.19.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: 5ad815c824cb9ddb441de9c4a34e76ed 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(>= 4.0), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 3.5), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 3.6), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: GPL (>= 3) MD5sum: 84918c377b25abecb5df6c5208923cf5 Package: mfa Version: 1.29.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: f41bbfd7aae1707d66fc435cf67b9adc Package: Mfuzz Version: 2.67.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 6dd0a7cd4c57f682ca75f101185beed0 Package: MGFM Version: 1.41.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: da926c6ad91c07a4c06a2e14d176d200 Package: MGFR Version: 1.33.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: a31b388512cc5d3a104fb8847afa6ae3 Package: MGnifyR Version: 1.3.0 Depends: R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment, SummarizedExperiment, BiocGenerics Imports: mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors, urltools, utils, tidyjson Suggests: biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick License: Artistic-2.0 | file LICENSE MD5sum: 8602a497bc77f59c35bf86f5b6dea2af Package: mgsa Version: 1.55.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: fa5bae203e74cfb94b15d81988032e62 Package: mia Version: 1.15.6 Depends: R (>= 4.0), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3) Imports: ape, BiocGenerics, BiocParallel, Biostrings, bluster, DECIPHER, decontam, DelayedArray, DelayedMatrixStats, DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics, mediation, methods, rbiom, rlang, S4Vectors, scater, scuttle, stats, tibble, tidyr, utils, vegan Suggests: ade4, BiocStyle, biomformat, dada2, knitr, miaViz, microbiomeDataSets, NMF, patchwork, phyloseq, reldist, rhdf5, rmarkdown, stringr, testthat, topicdoc, topicmodels, yaml License: Artistic-2.0 | file LICENSE MD5sum: 9a6289fe72e47ffa3108e7d64b1282a3 Package: miaSim Version: 1.13.0 Depends: TreeSummarizedExperiment Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE MD5sum: e3ad04a3a02edd1e37e40d1f0e238a90 Package: miaViz Version: 1.15.2 Depends: R (>= 4.0), ggplot2, ggraph (>= 2.0), mia (>= 1.13.0), SummarizedExperiment, TreeSummarizedExperiment Imports: ape, BiocGenerics, BiocParallel, DelayedArray, DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggplot2, ggraph, ggtree, methods, rlang, scater, S4Vectors, SingleCellExperiment, stats, tibble, tidygraph, tidyr, tidytext, tidytree, viridis Suggests: BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, knitr, patchwork, rmarkdown, testthat, vegan License: Artistic-2.0 | file LICENSE MD5sum: 67ecb5f22f4205dbebb9e7080faf2150 Package: MiChip Version: 1.61.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: b0ec6492bc24fc45f42c02a9c2cc5465 Package: microbiomeDASim Version: 1.21.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: 14894902b8065515feb448d89af32540 Package: MicrobiomeProfiler Version: 1.13.0 Depends: R (>= 4.2.0) Imports: clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils, yulab.utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: addd626903c34658c1afb0523928310c Package: MicrobiotaProcess Version: 1.19.0 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager License: GPL (>= 3.0) MD5sum: cb54e169256704831166a6528f6ec638 Package: microSTASIS Version: 1.7.0 Depends: R (>= 4.2.0) Imports: BiocParallel, ggplot2, ggside, grid, rlang, stats, stringr, TreeSummarizedExperiment Suggests: BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) License: GPL-3 MD5sum: 874aad108f006165d1e66eadeaad65e7 Package: MICSQTL Version: 1.5.0 Depends: R (>= 4.3.0), SummarizedExperiment, stats Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle License: GPL-3 MD5sum: a713cb70b37748c058ad338cc7145a3a Package: miloR Version: 2.3.0 Depends: R (>= 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License: GPL MD5sum: 518be6a2205907acea7e1a938e639eef Package: MineICA Version: 1.47.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: e3509ff1d0cc1f96108c9b778b6cc39b Package: minet Version: 3.65.0 Imports: infotheo License: Artistic-2.0 MD5sum: 3b32f1360e65aaf6863a7701452687aa Package: minfi Version: 1.53.1 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: 4dcfbad0d880514edc74dd02b4e228ea Package: MiPP Version: 1.79.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 940800de74f9e569639af5bdf3cf5883 Package: miQC Version: 1.15.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 47870b7fa83ffedb541f442839fb47ae Package: MIRA Version: 1.29.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 074ea522f8a3382452d3826969446780 Package: MiRaGE Version: 1.49.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 7b444679508fb12155d5d87c7a246b5f Package: miRBaseConverter Version: 1.31.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: 40b1ae33759536bb30659540e7080bdb Package: miRcomp Version: 1.37.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: e123ad31f6f024212a787c05b546a1ee Package: mirIntegrator Version: 1.37.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 22536ce5fd2520a551e0996dd2533ec7 Package: miRLAB Version: 1.37.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) MD5sum: 300c2235df741afee3ac828c3407359a Package: miRNAmeConverter Version: 1.35.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 970c38aa713c310c7296a15651c491bc Package: miRNApath 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linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 533509493d4cca56afcf7895f7b231f3 Package: mirTarRnaSeq Version: 1.15.0 Depends: R (>= 4.1.0), ggplot2 Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils, viridis Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE License: MIT + file LICENSE MD5sum: ab1ea0908b7bc36e7bda807b1c1935cd Package: missMethyl Version: 1.41.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2manifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: 5c35153bfb55b23fa542aa8db35a4d9d Package: missRows Version: 1.27.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 2b45e894ab0060c075f3bc5e1db83c22 Package: mitch Version: 1.19.3 Depends: R (>= 4.4) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra Suggests: stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: CC BY-SA 4.0 + file LICENSE MD5sum: b7d5162770f04b007291a534d2965617 Package: mixOmics Version: 6.31.4 Depends: R (>= 4.4.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils, gsignal, rgl Suggests: BiocStyle, knitr, rmarkdown, testthat, microbenchmark, magick License: GPL (>= 2) MD5sum: 468a86ed71f11db147dcb0910f95d00d Package: MLInterfaces Version: 1.87.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat Enhances: parallel License: LGPL MD5sum: 1dad49fd9a06accf82afc17f3ec00161 Package: MMDiff2 Version: 1.35.0 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: a5e5b93ea430c7178885c834e3e811cb Package: MMUPHin Version: 1.21.0 Depends: R (>= 3.6) Imports: Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: 5f604485635d53efaaf9c1a0c53beab7 Package: mnem Version: 1.23.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 MD5sum: 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Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 431d0cb14a8d41bddb157907337be3cc Package: MOFA2 Version: 1.17.0 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi Suggests: knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown License: file LICENSE MD5sum: d3f71dff8dabfc6c652e391cbdeca153 Package: MOGAMUN Version: 1.17.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 5e23e7959275db92e17905a952c89f2f Package: mogsa Version: 1.41.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: 28fad0833067c47d42f5129be1fcd108 Package: MoleculeExperiment Version: 1.7.0 Depends: R (>= 2.10) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 2ed29623d038af7e8b9913105af6992f Package: MOMA Version: 1.19.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: f2edb5c06e71337a5b34cf02097258a3 Package: monocle Version: 2.35.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: 75489dbaa2a535416ab74207c3df2033 Package: MoonlightR Version: 1.33.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR License: GPL (>= 3) MD5sum: b7db3f2707cb96cd161949efa07232fc Package: mosaics Version: 2.45.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: fa100027b2e5d0dc2be4b904e49aea64 Package: mosbi Version: 1.13.0 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 2d529b4503e7e435d037913fc2831470 Package: MOSClip Version: 1.1.0 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, methods, survminer, graph, graphite, AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap, survival, RColorBrewer, SuperExactTest, reshape, NbClust, S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap, FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase, ggplotify, qpgraph, org.Hs.eg.db, Matrix Suggests: RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 62f12d5edcb6fb6cfa654e9b7612f1d2 Package: Motif2Site Version: 1.11.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 MD5sum: f1a50eef3236748ce4649cb006149223 Package: motifcounter Version: 1.31.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: dffa1006be81110ff147eb6d7f3fb5e1 Package: motifTestR Version: 1.3.3 Depends: Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0), Imports: GenomeInfoDb, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif, Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0), VGAM License: GPL-3 MD5sum: 4d7d46935b6ed9a94beab7edd70e8117 Package: MouseFM Version: 1.17.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 83ed8a7aecd24d9cadf1e1a716aca0a7 Package: MPFE Version: 1.43.0 License: GPL (>= 3) MD5sum: efdf382c2db3496d365bd56ec04884a8 Package: mpra Version: 1.29.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 191fc7457e11b85faf3c1a4812ebd94b Package: MPRAnalyze Version: 1.25.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 MD5sum: 5da68cc98e71d2d9e3961b8d9b6b5e01 Package: msa Version: 1.39.0 Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign License: GPL (>= 2) MD5sum: 94ae4ad310c53d095b05527d4832fa95 Package: MSA2dist Version: 1.11.1 Depends: R (>= 4.4.0) Imports: Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, pwalign, rlang, seqinr, stats, stringi, stringr, tibble, tidyr, utils LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE MD5sum: 64a0b6e17bbdc881c05b697b75a1ea40 Package: MsBackendMassbank Version: 1.15.2 Depends: R (>= 4.0), Spectra (>= 1.15.10) Imports: BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>= 1.35.3), MsCoreUtils, DBI, utils Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown License: Artistic-2.0 MD5sum: 5e6b79ad29bb266a15de34850af6ee0e Package: MsBackendMetaboLights Version: 1.1.0 Depends: R (>= 4.2.0), Spectra (>= 1.15.12) Imports: curl, ProtGenerics, BiocFileCache, S4Vectors, methods Suggests: testthat, rmarkdown, mzR, knitr, BiocStyle License: Artistic-2.0 MD5sum: d05f0310f55e13fbd6dd5cd1713d9f79 Package: MsBackendMgf Version: 1.15.2 Depends: R (>= 4.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: effe65aff14e16b1e4b0f6254ccbe8d5 Package: MsBackendMsp Version: 1.11.1 Depends: R (>= 4.1.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: 84a5d07530969e8874df6d27096fa175 Package: MsBackendRawFileReader Version: 1.13.1 Depends: R (>= 4.1), methods, Spectra (>= 1.15.10) Imports: ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges, rawrr (>= 1.13.1), utils, BiocParallel Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: 1f539166ed53bbb965b45caef449d02d Package: MsBackendSql Version: 1.7.2 Depends: R (>= 4.2.0), Spectra (>= 1.15.10) Imports: BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3), DBI, MsCoreUtils, IRanges, data.table, progress, stringi, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR License: Artistic-2.0 MD5sum: be9b0d703441433a1e0cd7ede3923526 Package: MsCoreUtils Version: 1.19.0 Depends: R (>= 3.6.0) Imports: methods, S4Vectors, MASS, stats, clue LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest Enhances: HDF5Array License: Artistic-2.0 MD5sum: 590f858a989cc7a5d49325312ae772a3 Package: MsDataHub Version: 1.7.0 Imports: ExperimentHub, utils Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3) License: Artistic-2.0 MD5sum: ba9cb3a260a3b5d3770a918b354cf911 Package: MsExperiment Version: 1.9.0 Depends: R (>= 4.2), ProtGenerics (>= 1.35.2), Imports: methods, S4Vectors, IRanges, Spectra, SummarizedExperiment, QFeatures, DBI, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite License: Artistic-2.0 MD5sum: 027994c89db40f8695d34e8fb7cc8077 Package: MsFeatures Version: 1.15.0 Depends: R (>= 4.1) Imports: methods, ProtGenerics (>= 1.23.5), MsCoreUtils, SummarizedExperiment, stats Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2cbac4f994e554e9557f23b208ba39f1 Package: msgbsR Version: 1.31.0 Depends: R (>= 3.5.0), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: 4398278d3dbf40cb6757db6cd80dc910 Package: msmsEDA Version: 1.45.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 MD5sum: 6c2dda8b2b8cc1db2f6e3b8e7dd6f775 Package: msmsTests Version: 1.45.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: 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heatmaply, readr, rstatix, tibble, ggpubr Suggests: knitr, testthat (>= 3.0.0), downloadthis, DT, rmarkdown, BiocStyle, imputeLCMD License: MIT + file LICENSE MD5sum: 05685e86c95df1cf7c9a25f1b33f6587 Package: msqrob2 Version: 1.15.0 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr License: Artistic-2.0 MD5sum: fb516ab164ee7d65a0952dabdaaf7fee Package: MsQuality Version: 1.7.1 Depends: R (>= 4.2.0) Imports: BiocParallel (>= 1.32.0), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), msdata (>= 0.32.0), MsExperiment (>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics (>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.5.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra (>= 1.13.2), stats (>= 4.2.0), 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Rcpp, Biostrings, checkmate, ggrepel LinkingTo: Rcpp Suggests: knitr, rmarkdown, tinytest, covr, mockery, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: e8533de2a4b27de738be5d398d89abfb Package: MSstatsQC Version: 2.25.0 Depends: R (>= 3.5.0) Imports: dplyr,plotly,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 MD5sum: b4f987323cd289678cda039503215e32 Package: MSstatsQCgui Version: 1.27.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid Suggests: knitr License: Artistic License 2.0 MD5sum: 23a42b1e69e6c011a38fb473d3585faa Package: MSstatsShiny Version: 1.9.0 Depends: R (>= 4.2) Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2,plotly, data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics,mockery Suggests: rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 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(>= 3.5.0) Imports: Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges, IRanges, methods, S4Vectors, tidyr, utils Suggests: BiocStyle, HDF5Array, knitr, maftools, R.rsp, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR License: Artistic-2.0 MD5sum: 3e51e92831fef28a68c4e681211d4e84 Package: MultiBaC Version: 1.17.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods, plotrix, grDevices, pcaMethods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: 780b5036e6dd7dc1a606576df929e994 Package: multiClust Version: 1.37.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 622d995ec2f04b5a4b1a7c7d659706f9 Package: MultiDataSet Version: 1.35.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: 717164d51ede1bdced828e8f0b54d09c Package: multiGSEA Version: 1.17.3 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: bb49eebe567e5f1a1033860fc5f9cebe Package: multiHiCcompare Version: 1.25.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: c85abcea3a7f1b19e311ab7272a83f53 Package: MultiMed Version: 2.29.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: 37c4a27f18f010e96aed939fee266636 Package: multiMiR Version: 1.29.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 2.0), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: a644bf95719eafea7dd435cbc3ad3257 Package: MultimodalExperiment Version: 1.7.0 Depends: R (>= 4.3.0), IRanges, S4Vectors Imports: BiocGenerics, MultiAssayExperiment, methods, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: ad6aa0c4c9c90a6db19ff2881f7cf8b2 Package: multiscan Version: 1.67.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: 448d25966d8b2ac2b3e3ad890fb6423b Package: multistateQTL Version: 1.3.1 Depends: QTLExperiment, SummarizedExperiment, ComplexHeatmap, data.table, collapse Imports: methods, S4Vectors, grid, dplyr, tidyr, matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices Suggests: testthat, BiocStyle, knitr, covr, rmarkdown License: GPL-3 MD5sum: bb179b0e80a861fba0ac34ea47fb6ca1 Package: multiWGCNA Version: 1.5.0 Depends: R (>= 4.3.0), ggalluvial Imports: stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan License: GPL-3 MD5sum: 5bd27b5246c33e835da5770ee1bef01a Package: multtest Version: 2.63.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: fecdfa1dab8b6572bcfadd0eba10cc35 Package: MVCClass Version: 1.81.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 0ccd7d59b44ac947fe9da8f39286d667 Package: MWASTools Version: 1.31.0 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reshape, reshape2, penalized, parallel, doParallel, foreach, ggplot2, ggdendro, grid, MASS, assertthat, tidyr, methods, dplyr, graphics Suggests: testthat (>= 2.1.0), knitr, rmarkdown, pkgdown License: GPL-3 MD5sum: a8a22fbe490cf28323544a7ccb44c687 Package: NewWave Version: 1.17.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: 18dc33375ed02178ee4a0471a9071d2c Package: ngsReports Version: 2.9.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.5.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm License: LGPL-3 MD5sum: 6ce6c034790f5467d996caa1abad48d8 Package: nipalsMCIA Version: 1.5.2 Depends: R (>= 4.3.0) Imports: ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) License: GPL-3 MD5sum: cca3e0e75cdb1fb21dd732311217f5cb Package: nnNorm Version: 2.71.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 1e9b03c0b7062d6927d52de88762ab0d Package: nnSVG Version: 1.11.0 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: 9bca9fdc16853732743d9137fb436d5a Package: NOISeq Version: 2.51.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: caa072469d009532431085ecf868efee Package: normalize450K Version: 1.35.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 86af68bfba39a2fe5a4af1253f69b3bd Package: NormalyzerDE Version: 1.25.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: a7673e76f5efe0f307d324c8f845c54f Package: NormqPCR Version: 1.53.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 48203e609e31729f2720cee37c85e0a6 Package: NPARC Version: 1.19.0 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S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: 5a3887335206f721cdda2daa31bb2b19 Package: nuCpos Version: 1.25.0 Depends: R (>= 4.2.0) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: GPL-2 MD5sum: dd56f557441a7dd5817853bd699ca91d Package: nullranges Version: 1.13.0 Imports: stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt, DiagrammeR, tidySummarizedExperiment License: GPL-3 MD5sum: ac70390ab6c6d38f1aacebca180bb791 Package: NuPoP Version: 2.15.0 Depends: R (>= 4.0) Imports: graphics, utils Suggests: knitr, 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Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE MD5sum: 640d26b8614dffde441021e8b5e129bc Package: omicRexposome Version: 1.29.0 Depends: R (>= 3.5.0), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: 4388ccad597f8a3904584142b89d2fe3 Package: omicsPrint Version: 1.27.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: d84a258d7cac4c49520c3152baaf439a Package: omicsViewer Version: 1.11.0 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7788a78a887fe37d67205f59a281f54a Package: omXplore Version: 1.1.0 Depends: R (>= 4.4.0), methods Imports: shiny, MSnbase, PSMatch, SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, DT, RColorBrewer, gplots, highcharter, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph License: Artistic-2.0 MD5sum: 9c5c17d1da69036a2873748d664ba6a8 Package: oncomix Version: 1.29.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 04fa508e044e0c884637b41c13126c5f Package: oncoscanR Version: 1.9.0 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 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flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS MD5sum: d854a5e87fe5b9dc4e1ab5d66d0f9e2d Package: openPrimeR Version: 1.29.0 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), pwalign, XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), grDevices (>= 3.1.0), stats (>= 3.1.0), utils (>= 3.1.0), methods (>= 3.1.0) Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) License: 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MD5sum: 752bfbe5d3db8661a0df9fe01155487d Package: optimalFlow Version: 1.19.0 Depends: dplyr, optimalFlowData, rlang (>= 0.4.0) Imports: transport, parallel, Rfast, robustbase, dbscan, randomForest, foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 017ff50624dbd534d8be18360875ed8b Package: OPWeight Version: 1.29.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: a01cf6ef840331d3dc77e2008ac7409b Package: Organism.dplyr Version: 1.35.0 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: 9a3b2e6b36f5b1f37686a71c97bc68a2 Package: OrganismDbi Version: 1.49.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges (>= 1.31.13), txdbmaker Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 MD5sum: 1bfb1e3b052003a10d9ed7ad16659bf0 Package: orthogene Version: 1.13.0 Depends: R (>= 4.1) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, grr, repmis, ggtree, tools Suggests: rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB License: GPL-3 MD5sum: e086506546064ea3ee91ffb098f700d3 Package: orthos Version: 1.5.0 Depends: R (>= 4.3), SummarizedExperiment Imports: AnnotationHub, basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2, ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras, methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: cfdac813caf3d0673433484485fbd8a9 Package: OSAT Version: 1.55.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 98c46032c84149cf4897e10411b0c4df Package: Oscope Version: 1.37.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: 69c0ed6dd117746aad87fb45dd31d504 Package: OTUbase Version: 1.57.0 Depends: R (>= 2.9.0), 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Version: 2.19.0 Depends: ggplot2, ggrepel Imports: lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown License: GPL-3 MD5sum: ff822495f3fdb1f7bfa2bfa21611721c Package: PDATK Version: 1.15.0 Depends: R (>= 4.1), SummarizedExperiment Imports: data.table, MultiAssayExperiment, ConsensusClusterPlus, igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro, CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics, survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel, rlang, piano, scales, survcomp, genefu, ggplot2, switchBox, reportROC, pROC, verification, utils Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array License: MIT + file LICENSE MD5sum: 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Matrix, S4Vectors, shiny, readxl, shinyWidgets, htmlwidgets, DT, gridExtra, data.table, plotly, colourpicker, shinytoastr, scales, shinycssloaders Suggests: diffviewer, testthat (>= 3.0.0), vdiffr, rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, covr, devtools, R.devices, usethis, magick License: Artistic-2.0 MD5sum: 2226f54f49892b316ce3c9f77f33623b Package: pengls Version: 1.13.0 Depends: R (>= 4.2.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 MD5sum: 3a8fa3f369d6a6f320422d5cd5f18d9a Package: PepSetTest Version: 1.1.0 Imports: dplyr, limma, lme4, MASS, matrixStats, reshape2, stats, tibble, SummarizedExperiment, methods Suggests: statmod, BiocStyle, knitr, rmarkdown, tidyr License: GPL (>= 3) MD5sum: 765723829ae995923d9b117e80e95a7b Package: PepsNMR Version: 1.25.0 Depends: R (>= 3.6) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData License: GPL-2 | file LICENSE MD5sum: 8ff52f9e8103458063cf5bd2736fb988 Package: pepStat Version: 1.41.0 Depends: R (>= 3.0.0), Biobase, IRanges Imports: limma, fields, GenomicRanges, ggplot2, plyr, tools, methods, data.table Suggests: pepDat, Pviz, knitr, shiny License: Artistic-2.0 MD5sum: 8a11b3225c5ed8de0d27f48979d67c5f Package: pepXMLTab Version: 1.41.0 Depends: R (>= 3.0.1) Imports: XML(>= 3.98-1.1) Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 800fbb5eaaa33d1d447dfb851a2b3724 Package: pfamAnalyzeR Version: 1.7.0 Depends: R (>= 4.3.0), readr, stringr, dplyr Imports: utils, tibble, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 42bd244e15214b90333749f2c5f19108 Package: pgca Version: 1.31.0 Imports: utils, stats Suggests: knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 5437b78bfb90c946405ccd4375365a71 Package: pgxRpi Version: 1.3.2 Depends: R (>= 4.2) Imports: utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel, future, future.apply Suggests: BiocStyle, rmarkdown, knitr, testthat License: Artistic-2.0 MD5sum: 8736d5857870f4c2304f11ec20a1249c Package: phantasusLite Version: 1.5.0 Depends: R (>= 4.2) Imports: data.table, rhdf5client(>= 1.25.1), httr, stringr, stats, utils, Biobase, methods Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery License: MIT + file LICENSE MD5sum: 6b9d3224bd86d91314ae49214fb74719 Package: PharmacoGx Version: 3.11.1 Depends: R (>= 3.6), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: 4d7f1756ca554596ed5d8a81e5d427fb Package: PhenoGeneRanker Version: 1.15.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: 373209167c4e4e290d277309c3bdf8bd Package: phenomis Version: 1.9.0 Depends: SummarizedExperiment Imports: Biobase, biodb, biodbChebi, data.table, futile.logger, ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets, igraph, limma, methods, MultiAssayExperiment, MultiDataSet, PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble, tidyr, utils, VennDiagram Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 66281cce417d03c5a4189ef1db5677ab Package: phenopath Version: 1.31.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: 0d1aef2f199bbb54e2b8b5a5de671771 Package: phenoTest Version: 1.55.0 Depends: R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: f954a16d2dd63f243f2c32b787053656 Package: PhenStat Version: 2.43.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: 771bf809a475828d0e4a4a07384568e2 Package: philr Version: 1.33.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: caa25096ca1f608b824aade656777f13 Package: PhIPData Version: 1.15.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: 8d8c2442ed22a17e125e066c3e9c1df4 Package: phosphonormalizer Version: 1.31.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 138e36ee8dca3d19905ae55f458394b0 Package: PhosR Version: 1.17.0 Depends: R (>= 4.2.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: e26e97b346762dc18d52d134eaa787f4 Package: PhyloProfile Version: 1.99.1 Depends: R (>= 4.4.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, dplyr, DT, energy, ExperimentHub, extrafont, fastcluster, ggplot2, gridExtra, pbapply, plotly, RColorBrewer, RCurl, Rfast, scattermore, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: 08933f27065ed4a458894e949f66daf6 Package: piano Version: 2.23.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 7a5877d15b8e02d136c449494c3a84ae Package: pickgene Version: 1.79.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 3038a7d8a3fbbc8aabbd063c98cadaaa Package: Pigengene Version: 1.33.0 Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.28.0) Imports: bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI, DOSE Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy License: GPL (>= 2) MD5sum: ff8af22362fc7506898a2fbae84951af Package: pipeFrame Version: 1.23.0 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: e335e58ce93408924519a1112da14c2f Package: PIPETS Version: 1.3.0 Depends: R (>= 4.4.0) Imports: dplyr, utils, stats, GenomicRanges, BiocGenerics, methods Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 6664a5cca68cb427d62ff881431ac3e3 Package: Pirat Version: 1.1.0 Depends: R (>= 4.4.0) Imports: basilisk, reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors Suggests: knitr, BiocStyle License: GPL-2 MD5sum: 5458d66e04b15d771105f2f915d6f01c Package: PIUMA Version: 1.3.0 Depends: R (>= 4.3), ggplot2 Imports: cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales, Hmisc, patchwork, grDevices, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-3 + file LICENSE MD5sum: cd9266f4eb8a3ae3a81d3b4b6d24ca41 Package: planet Version: 1.15.0 Depends: R (>= 4.3) Imports: methods, tibble, magrittr, dplyr Suggests: ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown License: GPL-2 MD5sum: 74d7788d797a2bce2c19c32a1875c358 Package: planttfhunter Version: 1.7.0 Depends: R (>= 4.2.0) Imports: Biostrings, SummarizedExperiment, utils, methods Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: a9f9b57687358ef06e4252dcc3c17bc1 Package: plasmut Version: 1.5.0 Depends: R (>= 4.3.0) Imports: tibble, stats, dplyr Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5afc1994e93ec13e6f0c5464849874b8 Package: plgem Version: 1.79.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS, methods License: GPL-2 MD5sum: 0b3e1ffc46337b5a847eabf131810135 Package: plier Version: 1.77.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: f085418a816c34b6d686effe64197c9c Package: plotgardener Version: 1.13.0 Depends: R (>= 4.1.0) Imports: curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, glue, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rhdf5, rlang, stats, strawr, tools, utils, withr LinkingTo: Rcpp Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene License: MIT + file LICENSE MD5sum: 8237915f869737246b07380a55ab2d64 Package: plotGrouper Version: 1.25.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 MD5sum: e27ed1cf79a13b3a5fcb3e7299191710 Package: PLPE Version: 1.67.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: d41341ff34701651929bd9ab68dc38fc Package: PLSDAbatch Version: 1.3.0 Depends: R (>= 4.3.0) Imports: mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr, lmerTest, performance, grid, stats, pheatmap, vegan, Biobase, BiocStyle, TreeSummarizedExperiment Suggests: knitr, rmarkdown, testthat, badger License: GPL-3 MD5sum: b3659c466c4e177ef0590b978b45cca1 Package: plyinteractions Version: 1.5.0 Depends: R (>= 4.3.0) Imports: InteractionSet, GenomeInfoDb, BiocGenerics, GenomicRanges, plyranges, IRanges, S4Vectors, rlang, dplyr, tibble, tidyselect, methods, utils Suggests: tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings, BiocParallel, scales, HiContactsData, rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), RefManageR License: Artistic-2.0 MD5sum: e862fe4925d33637538e3d6de7a906d7 Package: plyxp Version: 1.1.0 Depends: R (>= 4.4.0) Imports: dplyr, purrr, rlang, SummarizedExperiment, tidyr, tidyselect, vctrs, tibble, pillar, cli, glue, S7, S4Vectors, utils, methods Suggests: devtools, knitr, rmarkdown, testthat, airway, IRanges, here License: MIT + file LICENSE MD5sum: 457c755ecd72aad06f0ccef7b80e25c3 Package: pmm Version: 1.39.0 Depends: R (>= 2.10) Imports: lme4, splines License: GPL-3 MD5sum: b3a25f6a497f7388f2ed3faf881470bf Package: PoDCall Version: 1.15.2 Depends: R (>= 4.5) Imports: ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT, LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: eebd8bd7fc0dfe6a6a34f6c1f82ae2fb Package: podkat Version: 1.39.0 Depends: R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges Imports: Rcpp (>= 0.11.1), parallel, stats (>= 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gplots (>= 3.1.1), S4Vectors (>= 0.30.0), parallel (>= 4.1.0), grDevices (>= 4.1.0), graphics (>= 4.1.0), stats (>= 4.1.0), utils (>= 4.1.0) Suggests: testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: 15611c8dd1f3ebb4a1de012409c58b62 Package: Polytect Version: 0.99.5 Depends: R (>= 4.4.0) Imports: stats, utils, grDevices, mvtnorm, sn, dplyr, flowPeaks, ggplot2, tidyverse, cowplot, mlrMBO, DiceKriging, smoof, ParamHelpers, lhs, rgenoud, BiocManager Suggests: testthat (>= 3.0.0), knitr, rmarkdown, ddPCRclust License: Artistic-2.0 MD5sum: 37a8dd1466b99ae331f18dcecf75116b Package: powerTCR Version: 1.27.0 Imports: cubature, doParallel, evmix, foreach, magrittr, methods, parallel, purrr, stats, truncdist, vegan, VGAM Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 1567238b418c55376e68c70b1c7ad61a Package: POWSC Version: 1.15.0 Depends: R (>= 4.1), Biobase, SingleCellExperiment, MAST Imports: pheatmap, ggplot2, RColorBrewer, grDevices, SummarizedExperiment, limma Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: 16b1fb098750c7fa6d23784628ff293a Package: ppcseq Version: 1.15.0 Depends: R (>= 4.1.0), rstan (>= 2.18.1) Imports: benchmarkme, dplyr, edgeR, foreach, ggplot2, graphics, lifecycle, magrittr, methods, parallel, purrr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rlang, rstantools (>= 2.1.1), stats, tibble, tidybayes, tidyr (>= 0.8.3.9000), utils LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: knitr, testthat, BiocStyle, rmarkdown License: GPL-3 MD5sum: 71457062c7eebe185777b72f119e360c Package: PPInfer Version: 1.33.0 Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData Imports: httr, grDevices, graphics, stats, utils License: Artistic-2.0 MD5sum: 3677bb6c14a98badd08a7ab53bb6ae2b Package: pqsfinder Version: 2.23.0 Depends: R (>= 3.5.0), Biostrings Imports: Rcpp 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qPLEXdata, rmarkdown, statmod, testthat, UniProt.ws, vdiffr License: GPL-2 MD5sum: 8c189288759ef5d99374e8524bb2c0dc Package: qsmooth Version: 1.23.0 Depends: R (>= 4.0) Imports: SummarizedExperiment, utils, sva, stats, methods, graphics, Hmisc Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: f21bf62792e59fa46a0bd0064b20a793 Package: QSutils Version: 1.25.0 Depends: R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods Imports: ape, stats, psych Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL-2 MD5sum: e176883b3e4e6fab7b656581e3825339 Package: qsvaR Version: 1.11.1 Depends: R (>= 4.2), SummarizedExperiment Imports: dplyr, sva, stats, ggplot2, rlang, methods Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 9e146874c79ce83838fcf619a8eec2d9 Package: QTLExperiment Version: 1.5.0 Depends: SummarizedExperiment Imports: methods, rlang, checkmate, 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rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db Enhances: BioMartGOGeneSets, UniProtKeywords License: MIT + file LICENSE MD5sum: f40cfcbccdebd6f3bedf75778ceb3fc6 Package: RGSEA Version: 1.41.0 Depends: R(>= 2.10.0) Imports: BiocGenerics Suggests: BiocStyle, GEOquery, knitr, RUnit License: GPL (>= 3) MD5sum: ac235ee8dbd570a84e6061879ff8dd48 Package: rhdf5 Version: 2.51.2 Depends: R (>= 4.0.0), methods Imports: Rhdf5lib (>= 1.13.4), rhdf5filters (>= 1.15.5) LinkingTo: Rhdf5lib Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel License: Artistic-2.0 MD5sum: 1e70c3b3b12150b2436c52731efa1a82 Package: rhdf5client Version: 1.29.0 Depends: R (>= 3.6), methods, DelayedArray Imports: httr, rjson, utils, data.table Suggests: knitr, testthat, BiocStyle, DT, rmarkdown License: Artistic-2.0 MD5sum: b6715277bd8ca86e4964e4aa62b4ca3e Package: rhdf5filters Version: 1.19.0 LinkingTo: Rhdf5lib Suggests: BiocStyle, knitr, rmarkdown, 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(>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) MD5sum: 3d322c2b3936791fd01819d32c87ba0f Package: RMassBank Version: 3.17.0 Depends: Rcpp Imports: assertthat, Biobase, ChemmineR, data.table, digest, dplyr, enviPat, glue, httr, httr2, logger, methods, MSnbase, mzR, purrr, R.utils, rcdk, readJDX, readr, rjson, S4Vectors, tibble, tidyselect, webchem, XML, yaml Suggests: BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown, RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1) License: Artistic-2.0 MD5sum: cb85247bad92cb04397bb1d8c297d0f1 Package: rmelting Version: 1.23.0 Depends: R (>= 3.6) Imports: Rdpack, rJava (>= 0.9-8) Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat License: GPL-2 | GPL-3 MD5sum: eea8b3077d93a62211257ed01bfb411a Package: RNAAgeCalc Version: 1.19.0 Depends: R (>= 3.6) Imports: ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 1ec2c247804c51cbeacdad9c35ee3100 Package: RNAdecay Version: 1.27.0 Depends: R (>= 3.5) Imports: stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr, scales Suggests: parallel, knitr, reshape2, rmarkdown License: GPL-2 MD5sum: 5c93406ef28b5e5cfb97117401ae39af Package: rnaEditr Version: 1.17.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, BiocGenerics, GenomeInfoDb, bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: adfd1ef276c29ceb9274953f8e34eb5e Package: RNAmodR.AlkAnilineSeq Version: 1.21.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data License: Artistic-2.0 MD5sum: e05ec5b95fdbd7becb754463273ebe45 Package: RNAmodR.ML Version: 1.21.0 Depends: R (>= 3.6), RNAmodR Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, stats, ranger Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras License: Artistic-2.0 MD5sum: 660a0a1de118cf9bf5094c93d05edff6 Package: RNAmodR.RiboMethSeq Version: 1.21.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data License: Artistic-2.0 MD5sum: f155dcddc80f4a37278deed59dd0fa8c Package: RNAsense Version: 1.21.0 Depends: R (>= 3.6) Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 89d2ea5ca998222901a422e83bdf3714 Package: rnaseqcomp Version: 1.37.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 8438cbc99d5d6d82654b391b2a9fc095 Package: RNAseqCovarImpute Version: 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IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame License: GPL-3 MD5sum: 4b602b442713cdaa3d29e21a3cd4dd1a Package: Rnits Version: 1.41.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: bb7a157d3d3f353da2e4845fadafbd34 Package: roastgsa Version: 1.5.0 Depends: R (>= 4.3.0) Imports: parallel, grDevices, graphics, utils, stats, methods, grid, RColorBrewer, gplots, ggplot2, limma, Biobase Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 License: GPL-3 MD5sum: a683d46692080130c1c68fa2807fd760 Package: ROC Version: 1.83.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: rmarkdown, Biobase, BiocStyle License: Artistic-2.0 MD5sum: 23bc77846e30d289d82a5ed91e5e8bf8 Package: ROCpAI Version: 1.19.0 Depends: boot, SummarizedExperiment, fission, knitr, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 54b89e20121559fee8b3454373612d61 Package: RolDE Version: 1.11.0 Depends: R (>= 4.2.0) Imports: stats, methods, ROTS, matrixStats, foreach, parallel, doParallel, doRNG, rngtools, SummarizedExperiment, nlme, qvalue, grDevices, graphics, utils Suggests: knitr, printr, rmarkdown, testthat License: GPL-3 MD5sum: 1142758787811575f6520552898ee414 Package: rols Version: 3.3.0 Depends: methods Imports: httr2, jsonlite, utils, Biobase, BiocGenerics (>= 0.23.1) Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, 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(>= 2.13.12), XVector (>= 0.19.7), bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE MD5sum: 3c9d1f94e4b0338017e016c6e795eb77 Package: rScudo Version: 1.23.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: 6e250721e366f1380a48a010ec95ce25 Package: rsemmed Version: 1.17.0 Depends: R (>= 4.0), igraph Imports: methods, magrittr, stringr, dplyr Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: fbdc99f9c28bc5ee3786c80739a93a93 Package: RSeqAn Version: 1.27.0 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Package: RTCGA Version: 1.37.0 Depends: R (>= 3.3.0) Imports: XML, RCurl, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales, rmarkdown, htmltools Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr License: GPL-2 MD5sum: d9c1603b0aedee9caa26aaecd45c9119 Package: RTCGAToolbox Version: 2.37.2 Depends: R (>= 4.3.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, httr, methods, RaggedExperiment, RCurl, RJSONIO, rvest, S4Vectors, stats, stringr, SummarizedExperiment, TCGAutils, utils Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: GPL-2 MD5sum: 4549fca81d259fbb90a87a25cf66b46f Package: RTN Version: 2.31.0 Depends: R (>= 3.6.3), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, 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License: GPL-2 MD5sum: d066df9bcd64e8748710d45eeb4d9dcd Package: RUVnormalize Version: 1.41.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: d00fb2b541433c0aa8b65c7d3215b000 Package: RUVSeq Version: 1.41.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: ced5067cf855650c2e14419acbc1d014 Package: Rvisdiff Version: 1.5.0 Depends: R (>= 4.3.0) Imports: edgeR, utils Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager License: GPL-2 | GPL-3 MD5sum: 9b2d12da2e6c5c2242c1de49f4373a1c Package: RVS Version: 1.29.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils, R.utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: 9c1f427e4446c2ce3b8a87c2ef258f2b Package: rWikiPathways Version: 1.27.0 Imports: httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr, readr, stringr, purrr, lubridate Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8dcaef99a9bf419a88ec6eb749df15fc Package: S4Arrays Version: 1.7.1 Depends: R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors, IRanges Imports: stats, crayon LinkingTo: S4Vectors Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 1f97f64a81472bc2c783e290177cde5a Package: S4Vectors Version: 0.45.2 Depends: R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>= 0.53.2) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: d1e69eb3f33423d9fd7b8ad2665dffb3 Package: safe Version: 3.47.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: 1a7a0474f7cf32b236ad27712a105d99 Package: sagenhaft Version: 1.77.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: ac104628d66977839cf3333516093f01 Package: SAIGEgds Version: 2.7.1 Depends: R (>= 3.5.0), gdsfmt (>= 1.28.0), SeqArray (>= 1.43.7), Rcpp Imports: methods, stats, utils, Matrix, RcppParallel, CompQuadForm, survey LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit, knitr, ggmanh, BiocGenerics License: GPL-3 MD5sum: 81deb38fb8d39a7d806e2d940f807d65 Package: sampleClassifier Version: 1.31.0 Depends: R (>= 4.0), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: c1af5f23a944fcd9b32eeb9013ccad18 Package: SamSPECTRAL Version: 1.61.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: 15f26d8ce9d030f7d3606b500986463d Package: sangeranalyseR Version: 1.17.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Suggests: testthat (>= 2.1.0) License: GPL-2 MD5sum: 70413b92c9a9f855d18dcd1663fb5154 Package: sangerseqR Version: 1.43.0 Depends: R (>= 3.5.0), Biostrings, pwalign, stringr Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 7fcd598eba88911dd2428f133fedc096 Package: SANTA Version: 2.43.0 Depends: R (>= 4.1), igraph Imports: graphics, Matrix, methods, stats Suggests: BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit License: GPL (>= 2) MD5sum: 60ba5d9d4dca1c8830076821f3771aae Package: SARC Version: 1.5.0 Depends: R (>= 4.3), RaggedExperiment, GenomicRanges Imports: tidyverse, utils, reshape2, DescTools, metap, multtest, plyranges, data.table, scales, RColorBrewer, grid, gtable, gridExtra, GenomicFeatures, stats, ggplot2, plotly, IRanges Suggests: knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments License: GPL-3 MD5sum: 0549e766285abdfd9de38884096930b0 Package: sarks Version: 1.19.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: 36f29c4ff8c82d497c8ed81708790777 Package: satuRn Version: 1.15.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 MD5sum: 7a6bc4cc9c923db1afa385c29c1f3844 Package: SBGNview Version: 1.21.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 MD5sum: 7160370c0b1a714580762abd890f6429 Package: SBMLR Version: 2.3.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: cf8f34b7eda52b06a0c19620effcb7fd Package: SC3 Version: 1.35.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater, BiocStyle License: GPL-3 MD5sum: 422ee08bc9b7a546415c4248d43b97c0 Package: Scale4C Version: 1.29.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 94e4a5c8271e55fd16f7300bd76ce22f Package: ScaledMatrix Version: 1.15.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats License: GPL-3 MD5sum: ebe5295bf96762c0dc56d2f464968fd5 Package: scanMiR Version: 1.13.0 Depends: R (>= 4.0) Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: c458eb9cfe1bd168f04c98d6c9f331aa Package: scAnnotatR Version: 1.13.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT 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MatrixGenerics, SparseArray, DelayedArray, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel, ggrastr Suggests: BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore License: GPL-3 MD5sum: 669ad940526128c77e4cd474e5a5d04d Package: scatterHatch Version: 1.13.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 4c06fc4257fbb8e034b5dc5b465157f7 Package: SCBN Version: 1.25.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown,BiocStyle,BiocManager License: GPL-2 MD5sum: f524d1a2fe55c215227f5f4f74e6f58e Package: scBubbletree Version: 1.9.0 Depends: R (>= 4.2.0) Imports: reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils, dplyr Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE MD5sum: 9ce47ddbf2870ec9c506746a1889798b Package: scCB2 Version: 1.17.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: e3eff63f23d235dfde9f482d6ea54318 Package: scClassify Version: 1.19.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: 6e7fbf9d769354dbadb31ec96b2a560d Package: sccomp Version: 1.11.0 Depends: R (>= 4.2.0) Imports: instantiate (>= 0.2.3), callr, fs, stats, SeuratObject, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, stats, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue, withr, digest Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, knitr, loo, prettydoc, tidyseurat, tidySingleCellExperiment, bayesplot, posterior License: GPL-3 MD5sum: b94017fe4b1bee9086304bccbc8b8f8e Package: scDataviz Version: 1.17.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 294e73dca5605439281251570e2e7690 Package: scDDboost Version: 1.9.1 Depends: R (>= 4.2), ggplot2 Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods LinkingTo: Rcpp, RcppEigen, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 2663ae1732b2e0b132874ba5cf218c02 Package: scde Version: 2.35.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: 2fccdd5b142aa222f8596f090e9cc2ac Package: scDesign3 Version: 1.5.0 Depends: R (>= 4.3.0) Imports: dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE MD5sum: c44bfc7e8165ddaec35951bc056a9b38 Package: scDiagnostics Version: 1.1.0 Depends: R (>= 4.4.0) Imports: SingleCellExperiment, methods, isotree, ggplot2, ggridges, SummarizedExperiment, ranger, transport, speedglm, cramer, rlang, bluster, patchwork Suggests: AUCell, BiocStyle, knitr, Matrix, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 86c576edeef39635499c52816616f0a6 Package: scDotPlot Version: 1.1.0 Depends: R (>= 4.4.0) Imports: aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree, grDevices, magrittr, purrr, rlang, scales, scater, Seurat, SingleCellExperiment, stats, stringr, tibble, tidyr Suggests: AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq, scuttle, SeuratObject, testthat, vdiffr License: Artistic-2.0 MD5sum: 2b41468b57747a4d7fedd07283667d07 Package: scds Version: 1.23.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE MD5sum: 701bbd4069c723eccfbdd0220ab3b1fd Package: SCFA Version: 1.17.0 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL MD5sum: 87ff8a71b1df25c0537a440e8eec80e0 Package: scFeatureFilter Version: 1.27.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: 066db759db2940220feb6b9d49a9ccf3 Package: scFeatures Version: 1.7.0 Depends: R (>= 4.2.0) Imports: DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, SingleCellSignalR, MatrixGenerics, Seurat, DT Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler License: GPL-3 MD5sum: 1a3f01b30a530a1c8e32118659bbe284 Package: schex Version: 1.21.0 Depends: SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1) Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle License: GPL-3 MD5sum: 1ceb1d410e2b7e508746be12693fd3b9 Package: scHOT Version: 1.19.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: 45daa7613ec3fa483dc56ad4a1f42d7a Package: scider Version: 1.5.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, rlang, isoband, S4Vectors, grDevices Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 93cb9c3f9643c8cf9507b2cb38f6df3e Package: scifer Version: 1.9.0 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods, basilisk, reticulate, here, utils, basilisk.utils Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) Enhances: parallel License: MIT + file LICENSE MD5sum: cb4669fcb2cca4e352ae4f3fed98fde9 Package: scmap Version: 1.29.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: c16be02d6ffde6be489e3975f463ef53 Package: scMET Version: 1.9.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 5a133f10e6601ad38c452dcd08e07f3d Package: scmeth Version: 1.27.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: f6088a8fe110cf612ccd754cb79a1e9d Package: scMitoMut Version: 1.3.1 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: 2ba8bca6fe894f1ba09ed8077d4fe5f9 Package: scMultiSim Version: 1.3.0 Depends: R (>= 4.4.0) Imports: foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment, BiocParallel Suggests: knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: d7792046457c7b996ccf70ae8fa7eaa6 Package: SCnorm Version: 1.29.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 179c2d014c4aec63759e9a4b7a7e7839 Package: scone Version: 1.31.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment, DelayedMatrixStats, sparseMatrixStats Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 2092c16a5c2f737bd79b557eece88895 Package: Sconify Version: 1.27.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: a2f9561d1de56d8912cde119781a9cee Package: SCOPE Version: 1.19.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: 55c82e51a5ff6b1fb0ccc978a4d7d5b4 Package: scoup Version: 1.1.4 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: 4c7027c4c07e7e7eeacf35879e5d2205 Package: scPCA Version: 1.21.0 Depends: R (>= 4.0.0) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 4f7f6e9f2524b757158cca337527c514 Package: scrapper Version: 1.1.12 Imports: methods, Rcpp, beachmat (>= 2.21.6), DelayedArray, BiocNeighbors (>= 1.99.0), igraph, parallel LinkingTo: Rcpp, assorthead, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, S4Vectors, SummarizedExperiment, SingleCellExperiment, scRNAseq License: MIT + file LICENSE MD5sum: b9450c600736c0b50ccd2a4a7ed282e3 Package: scReClassify Version: 1.13.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr License: GPL-3 + file LICENSE MD5sum: 885332202dedb0449eea9000f56afad1 Package: scRecover Version: 1.23.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 6235282fb1dc583260b833cb0f534d45 Package: screenCounter Version: 1.7.1 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: fb5e6dc3ae66b5a987e520178d1221e4 Package: ScreenR Version: 1.9.0 Depends: R (>= 4.2) Imports: methods (>= 4.0), rlang (>= 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eeae59cf27b47cde89f14bf2024893fd Package: scry Version: 1.19.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: 79b328c1ff6c8c75e98513802232e835 Package: scShapes Version: 1.13.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5286d457fc80a22d415e1fa1b8494d95 Package: scTensor Version: 2.17.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens, AnnotationHub License: Artistic-2.0 MD5sum: 2f40d4d66d3312d1d424c0cba961e4af Package: scTGIF Version: 1.21.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: 09d08165c8fd945ce27576621ba75304 Package: scTHI Version: 1.19.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: d73e81c5f8685e8ecdf759fc1f6c1b70 Package: scuttle Version: 1.17.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran License: GPL-3 MD5sum: ad7e2beb907e25033a7031d703b3e92b Package: scviR Version: 1.7.0 Depends: R (>= 4.3), basilisk, shiny, SingleCellExperiment Imports: reticulate, BiocFileCache, utils, pheatmap, SummarizedExperiment, S4Vectors, limma, scater, stats, MatrixGenerics Suggests: knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle License: Artistic-2.0 MD5sum: d6d9321fdc61b258e15b8cddf166c51b Package: SDAMS Version: 1.27.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 8b3e0a78348486149505c95b74fc4c10 Package: seahtrue Version: 1.1.0 Depends: R (>= 4.2.0) Imports: dplyr (>= 1.1.2), readxl (>= 1.4.1), logger (>= 0.2.2), tidyxl (>= 1.0.8), purrr 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TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 MD5sum: c0ccc17792699efe25424ae2a377ac55 Package: segmentSeq Version: 2.41.1 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: c6c45c2ca74d45a5daad058d17335bb9 Package: selectKSigs Version: 1.19.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 81396a2c75e79d001ecbaba78491b3ab Package: SELEX Version: 1.39.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: ea4ad0529ce081220d9bc4a701283b35 Package: SemDist Version: 1.41.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: a8331ec497d40a2a62bd2d0af56f4e5c Package: semisup Version: 1.31.0 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: d951a332a9c1b78a441b43d8eb2af781 Package: seq.hotSPOT Version: 1.7.0 Depends: R (>= 3.5.0) Imports: R.utils, hash, stats, base, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 02f0913ac1a012bd9a51691d5bafd7bb Package: seq2pathway Version: 1.39.0 Depends: R (>= 3.6.2) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: 7f377ae6b312c2c22b04e53e9cdca286 Package: seqArchR Version: 1.11.0 Depends: R (>= 4.2.0) Imports: utils, graphics, cvTools (>= 0.3.2), MASS, Matrix, methods, stats, cluster, matrixStats, fpc, cli, prettyunits, reshape2 (>= 1.4.3), reticulate (>= 1.22), BiocParallel, Biostrings, grDevices, ggplot2 (>= 3.1.1), ggseqlogo (>= 0.1) Suggests: cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 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GPL-3 MD5sum: 2b99de55ae054cc1191a6edc9bd890d0 Package: seqcombo Version: 1.29.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: 54e85d3a8789ea0e992f8d8adebc62b4 Package: SeqGate Version: 1.17.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 2cf4722f01a26002e1d2553232b94328 Package: seqLogo Version: 1.73.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: 55fc1f6c967f55278711300da58baa85 Package: seqPattern Version: 1.39.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 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wheatmap (>= 0.2.0), GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2 Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: 09d4279f4475571ee9a596c6ac257876 Package: sevenbridges Version: 1.37.0 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: dba65fda9e4697b3160a44cab28ab768 Package: SGCP Version: 1.7.0 Depends: R (>= 4.2.0) Imports: ggplot2, expm, caret, plyr, dplyr, GO.db, annotate, SummarizedExperiment, genefilter, GOstats, RColorBrewer, xtable, Rgraphviz, reshape2, openxlsx, ggridges, DescTools, org.Hs.eg.db, methods, grDevices, stats, RSpectra, graph Suggests: knitr, rmarkdown, BiocManager, devtools, BiocStyle License: GPL-3 MD5sum: 7a69fd82ffc26b5daec2cc5e3d91e365 Package: SharedObject Version: 1.21.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 02cace149681ed6e4f804d889bb4e6d8 Package: shiny.gosling Version: 1.3.0 Imports: htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest, rjson Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio License: LGPL-3 MD5sum: 6ce86ceb34556b05273b85727af5e89b Package: shinyMethyl Version: 1.43.0 Imports: Biobase, BiocGenerics, graphics, grDevices, htmltools, MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats, utils Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 7c815d57e598c6336d8d39cab80e8e08 Package: ShortRead Version: 1.65.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 MD5sum: 8706682fd427f37ab8c2e169ac51263d Package: SIAMCAT Version: 2.11.0 Depends: R (>= 4.2.0), mlr3, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 MD5sum: 2f5f860d328d17021c85292e23ba6b6d Package: SICtools Version: 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stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 75f47878142458e24dd27ab505214fb5 Package: sights Version: 1.33.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: ad5d2c30916eddeee3e570e466c6bfd7 Package: signatureSearch Version: 1.21.0 Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: eca210674ee75ba6165f4436aed1d083 Package: signifinder Version: 1.9.3 Depends: R (>= 4.3.0) Imports: AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV, cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges, GSVA, IRanges, magrittr, matrixStats, maxstat, methods, openair, org.Hs.eg.db, patchwork, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, SpatialExperiment, stats, scales, SummarizedExperiment, survival, survminer, viridis Suggests: BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 1d6d469b558486d92b1606f989f3be69 Package: sigsquared Version: 1.39.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 91282e4ccc5f2436346320edd1066869 Package: SIM Version: 1.77.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: 659c905908377a7b4c482fd05e004919 Package: SIMAT Version: 1.39.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: bf8c0b4235ff6cceab2ea83d1aafdb29 Package: SimBu Version: 1.9.0 Imports: basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr Suggests: curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 09e4a80b21bb719b5a6c784d73beec20 Package: SIMD Version: 1.25.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: 3cc00798f9bbf89f0a1897df81a6388c Package: SimFFPE Version: 1.19.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: 95df834db596cb4bf58f6063cedc0847 Package: similaRpeak Version: 1.39.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 684a5312a1a6c2d31c7b8645b64f59d1 Package: SIMLR Version: 1.33.0 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: 647112e32a07378272fd58b6d8c4db96 Package: simona Version: 1.5.0 Depends: R (>= 4.1.0) Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE MD5sum: 6a48b1755ef4b2a6981c790741ee7af0 Package: simPIC Version: 1.3.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, Matrix, stats, SummarizedExperiment, actuar, rlang, S4Vectors, methods, scales, scuttle Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: b262b14eaa0e557a67a1bb94c94a1c61 Package: simpleSeg Version: 1.9.0 Depends: R (>= 3.5.0) Imports: BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 MD5sum: babcad24f67f0b42ec47cb47ed8e3fb2 Package: simplifyEnrichment Version: 2.1.0 Depends: R (>= 4.0.0) Imports: simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong, digest, tm, GO.db, AnnotationDbi, slam, methods, clue, grDevices, stats, utils, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: 681c905f65199b0eea6d5788105b1abf Package: sincell Version: 1.39.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 6406e5182c39e559d0b8c3db699ea90d Package: SingleCellAlleleExperiment Version: 1.3.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 1ab88d4dd89bbc4642b307374772953f Package: SingleCellExperiment Version: 1.29.1 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: 78e718bdccde629b05fd5ecda5c0f72e Package: SingleR Version: 2.9.4 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>= 2.23.5) LinkingTo: Rcpp, beachmat, assorthead, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scrapper, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 MD5sum: bb6ac3e25cea756c8af1c75125e0825a Package: singscore Version: 1.27.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: a122e64cdd9f26a87ce2fe7a1e40bc83 Package: SiPSiC Version: 1.7.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle License: file LICENSE MD5sum: 55036cce42cf557625280b5228b76f10 Package: sitePath Version: 1.23.0 Depends: R (>= 4.1) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 0b9a2b6dd9aca5722f1925c083903d43 Package: sizepower Version: 1.77.0 Depends: stats License: LGPL MD5sum: 4383d9138b997800954eb32f73eccc05 Package: sketchR Version: 1.3.0 Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment License: MIT + file LICENSE MD5sum: 93bef61f08194386e8a0b57421982b41 Package: skewr Version: 1.39.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: 07ede8a74692ae19f0e35beb31217e2a Package: slingshot Version: 2.15.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: 3494936010785c6fdb241055640d9700 Package: SLqPCR Version: 1.73.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: f30bd562d076ac26229a3522f038fd4d Package: SMAD Version: 1.23.0 Depends: R (>= 3.6.0), RcppAlgos Imports: magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: ee5e38737118c5f993021c60dfc68bf9 Package: smartid Version: 1.3.2 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR License: MIT + file LICENSE MD5sum: 938be9ad905d7722d3425647f1652127 Package: SMITE Version: 1.35.0 Depends: R (>= 3.5), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: b739b4ecb599b05644af0facf870e8a8 Package: smoothclust Version: 1.3.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, sparseMatrixStats, spdep, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE MD5sum: 44ffea8d277e30f2959eb4b928c92aaa Package: smoppix Version: 0.99.34 Depends: R (>= 4.4.0) Imports: spatstat.geom(>= 3.2.0),spatstat.random,methods,BiocParallel,SummarizedExperiment,SpatialExperiment,scam,Rdpack,stats,utils,extraDistr,lmerTest,lme4,ggplot2,graphics,grDevices,Rcpp (>= 1.0.11),Matrix,spatstat.model,openxlsx LinkingTo: Rcpp Suggests: testthat,rmarkdown,knitr,DropletUtils,polyCub,RImageJROI,sp,ape,htmltools,funkycells,glmnet,doParallel License: GPL-2 MD5sum: 6d7ae2c0ede095eba5d25604a4e2e750 Package: SNAGEE Version: 1.47.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: 02b88b6c8793c8573af45551e60ac327 Package: snapcount Version: 1.19.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 08e8b5284015b128f1a60b084c5045fd Package: snifter Version: 1.17.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: 0facccef8e39c75209f33b111db75eb1 Package: snm Version: 1.55.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: f9e75d07f4b546bfc870f0af407039f6 Package: SNPediaR Version: 1.33.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: a109e40c71de18effafdb848fc46115f Package: SNPRelate Version: 1.41.0 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 MD5sum: af19a424a8f3ec1c620e1abaed0b36d4 Package: snpStats Version: 1.57.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc Suggests: hexbin License: GPL-3 MD5sum: f96fd4cafd49b7ea37ef6ea98335d377 Package: sosta Version: 0.99.3 Depends: R (>= 4.4.0) Imports: terra, sf, smoothr, spatstat.explore, spatstat.geom, SpatialExperiment, dplyr, ggplot2, patchwork, SummarizedExperiment, stats, rlang, parallel Suggests: knitr, rmarkdown, ggspavis, BiocStyle, imcdatasets, ggfortify, tidyr, testthat (>= 3.0.0) License: GPL (>= 3) + file LICENSE MD5sum: 0bb73b601a69e4a790a6f84dc7dfd573 Package: SpaceMarkers Version: 1.3.1 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix, qvalue, stats, utils, methods Suggests: data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS Enhances: BiocParallel License: MIT + file LICENSE MD5sum: 9a13b8e5530e2f67e307ad470801f319 Package: SpacePAC Version: 1.45.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: 39f643469aaa28697d5b6c5b48b1c37d Package: sparrow Version: 1.13.4 Depends: R (>= 4.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE MD5sum: c252ac2bf9ef025b2d1a1727bd845f25 Package: SparseArray Version: 1.7.4 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors (>= 0.43.2), S4Arrays (>= 1.5.11) Imports: utils, stats, matrixStats, IRanges, XVector LinkingTo: S4Vectors, IRanges, XVector Suggests: HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 739a550ba1db2e71f2b294712d93b725 Package: sparseMatrixStats Version: 1.19.0 Depends: MatrixGenerics (>= 1.5.3) Imports: Rcpp, Matrix, matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 2bdff26064c5bad5be7ef7f2e669fb76 Package: sparsenetgls Version: 1.25.0 Depends: R (>= 4.0.0), Matrix, MASS Imports: methods, glmnet, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 MD5sum: 241d45ba5df792430d36dd91ddf904b4 Package: SparseSignatures Version: 2.17.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2, RhpcBLASctl Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: 617fd5dfda44a916d2a403738915d896 Package: spaSim Version: 1.9.0 Depends: R (>= 4.2.0) Imports: ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown License: Artistic-2.0 MD5sum: f94b27faf6f5a442fcc4713ec150cc80 Package: SpatialCPie Version: 1.23.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), shiny (>= 1.1.0), shinycssloaders (>= 0.2.0), shinyjs (>= 1.0), shinyWidgets (>= 0.4.8), stats (>= 3.6.0), SummarizedExperiment (>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), tools (>= 3.6.0), utils (>= 3.5.0), zeallot (>= 0.1.0) Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) License: MIT + file LICENSE MD5sum: 5074ccc4e6cbf00acdeed9fe994c2e4a Package: spatialDE Version: 1.13.0 Depends: R (>= 4.3) Imports: reticulate, basilisk (>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, ggplot2, ggrepel, scales, gridExtra Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 1523a993429a4c588f901a4d53873174 Package: SpatialDecon Version: 1.17.0 Depends: R (>= 4.0.0) Imports: grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf, Seurat License: MIT + file LICENSE MD5sum: c4f4e4c8e2e9810ac2b408beae9b2862 Package: SpatialExperiment Version: 1.17.0 Depends: methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils License: GPL-3 MD5sum: e5cd0802775ca2ea8b510d7687c02492 Package: SpatialFeatureExperiment Version: 1.9.7 Depends: R (>= 4.2.0) Imports: Biobase, BiocGenerics, BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spatialreg, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot Suggests: arrow, BiocStyle, dplyr, knitr, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData (>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, Voyager (>= 1.7.2), withr, xml2 License: Artistic-2.0 MD5sum: df03c34dccf37d95d0398a1218a3fcee Package: spatialHeatmap Version: 2.13.1 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 MD5sum: c0104d6c21ae3749a012d7b4ec96b0f8 Package: SpatialOmicsOverlay Version: 1.7.0 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: c4bf6941b8cafdd1fc076c91757b66e0 Package: spatialSimGP Version: 1.1.0 Depends: R (>= 4.4) Imports: SpatialExperiment, MASS, SummarizedExperiment Suggests: testthat (>= 3.0.0), STexampleData, ggplot2, knitr License: MIT + file LICENSE MD5sum: 33001bc2e8264e611491586fc1b8a331 Package: speckle Version: 1.7.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 2086834fa088f974e0c197ceb0a1ac5a Package: specL Version: 1.41.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: 9d474421618e5efd616fa4eec18d3a96 Package: SpeCond Version: 1.61.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: 70d78853bcd2c88246f0e339a8b4ccce Package: Spectra Version: 1.17.5 Depends: R (>= 4.0.0), S4Vectors, 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methods, SummarizedExperiment, stats, utils, scuttle Suggests: testthat, STexampleData, knitr License: MIT + file LICENSE MD5sum: 57cefacb5aa2799ba246d4ca8bdd10c1 Package: SpotClean Version: 1.9.0 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 MD5sum: 5550a588300e3d26004d9080914e9887 Package: SPOTlight Version: 1.11.0 Depends: R (>= 4.1) Imports: ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, sparseMatrixStats, stats Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 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MD5sum: 38127f88e6140dac7fb06ff2298b6e14 Package: topconfects Version: 1.23.2 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2, scales, grid, grDevices Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle License: LGPL-2.1 | file LICENSE MD5sum: bbc9f695960aeaf7a8cb8eacf30a1ade Package: topdownr Version: 1.29.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2), MSnbase (>= 2.3.10), PSMatch (>= 1.6.0), ggplot2 (>= 2.2.1), mzR (>= 2.27.5) Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: 4992d021611ce1b185190c91a09c808c Package: topGO Version: 2.59.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 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stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: 1ded9e8d727ad5dd54fdce2f12ab7127 Package: tradeSeq Version: 1.21.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats License: MIT + file LICENSE MD5sum: 977743151f75f8d1e366839cfd252349 Package: TrajectoryGeometry Version: 1.15.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: 078545af5464effd255450bf1dc8745e Package: TrajectoryUtils Version: 1.15.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: df461a6195b6dc741b3bd22d62b2f407 Package: transcriptogramer Version: 1.29.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 779d0b9d70b2718447232cc3a9ca56f4 Package: transformGamPoi Version: 1.13.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: e6e31dc53b098e192643dc69bf8bf858 Package: transite Version: 1.25.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 213ed6196d759ef05d2f671a20500594 Package: transomics2cytoscape Version: 1.17.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 9bcc3eb197fc43e56c6260388edf56aa Package: traseR Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: 36eed14b8fe64a1982dede7e620d6e3b Package: traviz Version: 1.13.0 Depends: R (>= 4.0) Imports: ggplot2, viridis, mgcv, SingleCellExperiment, slingshot, princurve, Biobase, methods, RColorBrewer, SummarizedExperiment, grDevices, graphics, rgl Suggests: scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr License: MIT + file LICENSE MD5sum: 8a345fad2cedc445138eb4d767b2059d Package: TreeAndLeaf Version: 1.19.0 Depends: R(>= 4.0) Imports: RedeR(>= 1.40.4), igraph, ape Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer License: Artistic-2.0 MD5sum: b68931379fcaa6c243c1a6f68b653513 Package: treeclimbR Version: 1.3.1 Depends: R (>= 4.4.0) Imports: TreeSummarizedExperiment (>= 1.99.0), edgeR, methods, SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr, ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree, stats, utils, rlang Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: 658de87dcdd6ae4f9c03e4c614c48e3b Package: treeio Version: 1.31.0 Depends: R (>= 3.6.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6) Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 MD5sum: 3a60cec38b7c2e69ac746cff10cce407 Package: treekoR Version: 1.15.0 Depends: R (>= 4.1) Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) License: GPL-3 MD5sum: 746ef282d926591f0934eeab686f1549 Package: TreeSummarizedExperiment Version: 2.15.0 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: ef5aa2670bee82e51d9c924d6e9c478d Package: TREG Version: 1.11.0 Depends: R (>= 4.2), SummarizedExperiment Imports: Matrix, purrr, rafalib Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment License: Artistic-2.0 MD5sum: 6bc310e0cc30f4b47f8703448bac1c40 Package: Trendy Version: 1.29.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 8a4b36884fbaa3a873a4fc16cd08c5ac Package: tricycle Version: 1.15.0 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 2ebfca27fe66bfbc1309dcb95eb778d3 Package: TrIdent Version: 0.99.3 Depends: R (>= 4.2.0) Imports: graphics, utils, stats, dplyr, ggplot2, patchwork, stringr, tidyr, roll Suggests: BiocStyle, knitr, rmarkdown, kableExtra, testthat (>= 3.0.0) License: GPL-2 MD5sum: 3bdcb7809caf6445e15d44feb5ee97b4 Package: trio Version: 3.45.2 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1), data.table Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: be051c0e4e870c464f6c6647c1900a10 Package: triplex Version: 1.47.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: 01267773acffacd167d4f061597e90aa Package: tripr Version: 1.13.0 Depends: shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils, vegan Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr Enhances: parallel License: MIT + file LICENSE MD5sum: 89cf62b8307ee444ab3568598f21afcd Package: tRNA Version: 1.25.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: 0d5879d0494f3a798be57a7f1ff2f22e Package: tRNAdbImport Version: 1.25.0 Depends: R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges, utils Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: 859712d6ef9184a1272e569bcf54fd6b Package: TRONCO Version: 2.39.0 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick License: GPL-3 MD5sum: 1e9a2793559c9536d8c1add831380272 Package: TSAR Version: 1.5.0 Depends: R (>= 4.3.0) Imports: dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), ggpubr (>= 0.4.0), magrittr (>= 2.0.3), mgcv (>= 1.8.38), readxl (>= 1.4.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), utils (>= 4.3.1), shiny (>= 1.7.4.1), plotly (>= 4.10.2), shinyjs (>= 2.1.0), jsonlite (>= 1.8.7), rhandsontable (>= 0.3.8), openxlsx (>= 4.2.5.2), shinyWidgets (>= 0.7.6), minpack.lm (>= 1.2.3) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: f512672a2725c42be19cc726d2dcbf87 Package: TSCAN Version: 1.45.0 Depends: R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SparseArray (>= 1.5.23), DelayedArray (>= 0.31.9), S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: 35287cb45300b3d59d8e0395b4c38d51 Package: TTMap Version: 1.29.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: 81b68f3ca36e6231d57f816a00801311 Package: TurboNorm Version: 1.55.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata, hgu95av2cdf License: LGPL MD5sum: ea69748bb5811e48b83476f5af5439f6 Package: tweeDEseq Version: 1.53.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils LinkingTo: Rcpp Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 7551aacb526f444c44b8badfe0d8db51 Package: twoddpcr Version: 1.31.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: ec53731bfba93c9133b4206e992d6d13 Package: tximeta Version: 1.25.2 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools License: GPL-2 MD5sum: f995b7f02895e585ec3473b87abb8e09 Package: tximport Version: 1.35.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) MD5sum: 3c39e57ac68799a006e11e6befa685a1 Package: UCell Version: 2.11.1 Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: bde493cb3ec561ecd15597dcc6b8452d Package: UCSC.utils Version: 1.3.1 Imports: methods, stats, httr, jsonlite, S4Vectors Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 16347fd7f8d685c3a6e664ff4a3588a1 Package: Ularcirc Version: 1.25.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, plotgardener, R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: f9b8271e6ec8a3ee1f74f9c3b9a89ff6 Package: uncoverappLib Version: 1.17.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: d52e44acb0c33e68d2a7a33e0d142932 Package: UNDO Version: 1.49.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 6fb160a233814943835952f47a791b28 Package: unifiedWMWqPCR Version: 1.43.0 Depends: methods Imports: BiocGenerics, limma, stats, graphics License: GPL (>= 2) MD5sum: 1542c2680d683b97f872a870655a3126 Package: UniProt.ws Version: 2.47.6 Imports: AnnotationDbi, AnVILBase, BiocFileCache, BiocBaseUtils, BiocGenerics, httr2, jsonlite, methods, progress, rjsoncons, utils Suggests: BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 02a024a655709f10311d980ff94d7f1f Package: universalmotif Version: 1.25.1 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: 4d89b10e66c12402b6bc1742b663ae77 Package: updateObject Version: 1.11.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 99c09f0d7d95bbdad86a82848fa7265b Package: uSORT Version: 1.33.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: 827a388f777db1ce126095c767c9bbfd Package: VarCon Version: 1.15.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 9820f8ceb97d6f4380f81e370f140ae3 Package: variancePartition Version: 1.37.2 Depends: R (>= 4.3.0), ggplot2, limma (>= 3.62.1), BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: cc6449b9331d7cb95798168ee65947ec Package: VaSP Version: 1.19.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 4e795972c7c0f856e30d2dfab8e978d9 Package: vbmp Version: 1.75.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 63a1b76051c1c6321607971394de0a73 Package: VDJdive Version: 1.9.0 Depends: R (>= 4.2) Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: ab20a5546660fe5ccba5a59d24534db6 Package: VegaMC Version: 3.45.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: 2983b23e2215e107a2831736aa2b7f9a Package: velociraptor Version: 1.17.0 Depends: SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR License: MIT + file LICENSE MD5sum: 1c1808d40d120e832cda7ee0e9819d9a Package: veloviz Version: 1.13.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: dcee12fcc623d3cf345448279a9800db Package: VennDetail Version: 1.23.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat, markdown License: GPL-2 MD5sum: 6b7ad8c3eb1bcc59d681038e51632c44 Package: VERSO Version: 1.17.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 36d2614e42b8608bce94be85a9791fab Package: viper Version: 1.41.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: 395f61171fd4abfc3261554d4066b4c4 Package: ViSEAGO Version: 1.21.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim, ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods, plotly, processx, topGO, RColorBrewer, R.utils, scales, stats, UpSetR, utils Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager MD5sum: d6fc3bf2f290d10516ee41aa4863bab5 Package: VisiumIO Version: 1.3.3 Depends: R (>= 4.4.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment Suggests: arrow, BiocStyle, data.table, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 607cead0725acf673ed4d8b29a9e44d1 Package: vissE Version: 1.15.0 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 MD5sum: 3b6e0133921d897d1a3e88f90ea42364 Package: Voyager Version: 1.9.2 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3) Imports: BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, MatrixGenerics, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot Suggests: arrow, automap, BiocSingular, BiocStyle, cowplot, data.table, DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 License: Artistic-2.0 MD5sum: 50fc7f156d7d49b4b292c9b24fa0f598 Package: VplotR Version: 1.17.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) MD5sum: 4af87b1b4d65bb990e5d1099db8cde7c Package: vsclust Version: 1.9.10 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler, httr License: GPL-2 MD5sum: 858f0b2b6a6d974f6f04338ccf2dc5f3 Package: vsn Version: 3.75.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 MD5sum: 2cd94bb9b6a24aa5b881a04f82aeafbf Package: vtpnet Version: 0.47.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 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assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: c59c5348c1a921bfacd4bcfda56243e1 Package: widgetTools Version: 1.85.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 51d54ad5b492f1cd717c8bf19467b41a Package: wpm Version: 1.17.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 8f1d9d0405408bd4b828250eb4e5a520 Package: wppi Version: 1.15.0 Depends: R(>= 4.1) Imports: dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>= 2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr Suggests: knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: 887f9e9ee3c60354f1ea9225b4cc2203 Package: Wrench Version: 1.25.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: 9ff4ee8bbe114909b63c0ab7aeb171ca Package: xCell2 Version: 0.99.107 Depends: R (>= 4.0.0) Imports: SummarizedExperiment, SingleCellExperiment, Rfast, singscore, AnnotationHub, ontologyIndex, tibble, dplyr, BiocParallel, Matrix, minpack.lm, pracma, methods, readr, magrittr, progress, quadprog Suggests: testthat, knitr, rmarkdown, ggplot2, randomForest, tidyr, EnhancedVolcano License: GPL (>= 3) MD5sum: 7470cea9f32552514f7b43d5d6b8bdd6 Package: xcms Version: 4.5.2 Depends: R (>= 4.0.0), BiocParallel (>= 1.8.0) Imports: MSnbase (>= 2.29.3), mzR (>= 2.25.3), 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BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata License: GPL-2 MD5sum: 6d1b15610dc681b34964a4b1bc0f5882 Package: XDE Version: 2.53.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: 1c0e40974f90fe6d0863316f4df30896 Package: xenLite Version: 1.1.0 Depends: R (>= 4.1) Imports: SpatialExperiment, BiocFileCache, Matrix, S4Vectors, SummarizedExperiment, methods, utils, EBImage, shiny, HDF5Array, arrow, ggplot2, SingleCellExperiment, TENxIO, dplyr, graphics, stats Suggests: knitr, testthat, BiocStyle, yesno, terra, SpatialFeatureExperiment, SFEData, tiff License: 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BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: 98e4fe123abc082e20a4ef622c48ed4e Package: yamss Version: 1.33.0 Depends: R (>= 4.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: 6216efd7169c5990bdd15ca0c58a8904 Package: yarn Version: 1.33.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: cd93dc6cc46b2ab079443867131aef47 Package: zellkonverter Version: 1.17.0 Imports: basilisk, cli, DelayedArray, Matrix, methods, reticulate, S4Vectors, SingleCellExperiment (>= 1.11.6), SummarizedExperiment, utils Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rhdf5 (>= 2.45.1), rmarkdown, scRNAseq, spelling, testthat, withr License: MIT + file LICENSE MD5sum: a1e2e7870c791bb1cd5954f47f027ca0 Package: zenith Version: 1.9.0 Depends: R (>= 4.2.0), limma, methods Imports: variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr (>= 7.5.1), Rfast, ggplot2, tidyr, reshape2, progress, utils, Rdpack, stats Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit License: Artistic-2.0 MD5sum: 3a1ea461980deb280867517874e2a322 Package: zFPKM Version: 1.29.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE MD5sum: fa611fea95dce5ac4708179a73b80518 Package: zinbwave Version: 1.29.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats License: Artistic-2.0 MD5sum: 2124f872b63899f653f964ab9ecfb85f Package: zlibbioc Version: 1.53.0 Suggests: BiocStyle, knitr License: Artistic-2.0 + file LICENSE MD5sum: 745a3d9d0bcc16336d86a26867501d63