Package: annotation
Version: 1.30.0
Depends: R (>= 3.3.0), VariantAnnotation, AnnotationHub,
        Organism.dplyr, TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Mmusculus.UCSC.mm10.ensGene, org.Hs.eg.db, org.Mm.eg.db,
        Homo.sapiens, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome,
        TxDb.Athaliana.BioMart.plantsmart22
Suggests: knitr, rmarkdown, BiocStyle
License: Artistic-2.0
MD5sum: 38d539ed1832dfa2ae8bc2034865cecd
NeedsCompilation: no
Title: Genomic Annotation Resources
Description: Annotation resources make up a significant proportion of
        the Bioconductor project. And there are also a diverse set of
        online resources available which are accessed using specific
        packages.  This walkthrough will describe the most popular of
        these resources and give some high level examples on how to use
        them.
biocViews: AnnotationWorkflow, Workflow
Author: Marc RJ Carlson [aut], Herve Pages [aut], Sonali Arora [aut],
        Valerie Obenchain [aut], Martin Morgan [aut], Bioconductor
        Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer
        <maintainer@bioconductor.org>
URL: http://bioconductor.org/packages/annotation
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/annotation
git_branch: RELEASE_3_20
git_last_commit: e0c27c9
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/annotation_1.30.0.tar.gz
vignettes:
        vignettes/annotation/inst/doc/Annotating_Genomic_Ranges.html,
        vignettes/annotation/inst/doc/Annotation_Resources.html
vignetteTitles: Annotating Genomic Ranges, Genomic Annotation Resources
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/annotation/inst/doc/Annotating_Genomic_Ranges.R,
        vignettes/annotation/inst/doc/Annotation_Resources.R
dependencyCount: 122

Package: arrays
Version: 1.32.0
Depends: R (>= 3.0.0)
Suggests: affy, limma, hgfocuscdf, knitr, rmarkdown, BiocStyle
License: Artistic-2.0
MD5sum: 864b488ba4ae3d083a29dd2589f833b2
NeedsCompilation: no
Title: Using Bioconductor for Microarray Analysis
Description: Using Bioconductor for Microarray Analysis workflow
biocViews: Workflow, BasicWorkflow
Author: Bioconductor Package Maintainer [aut, cre]
Maintainer: Bioconductor Package Maintainer
        <maintainer@bioconductor.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/arrays
git_branch: RELEASE_3_20
git_last_commit: a6fd298
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/arrays_1.32.0.tar.gz
vignettes: vignettes/arrays/inst/doc/arrays.html
vignetteTitles: Using Bioconductor for Microarray Analysis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/arrays/inst/doc/arrays.R
dependencyCount: 0

Package: BiocMetaWorkflow
Version: 1.28.0
Suggests: BiocStyle, knitr, rmarkdown, BiocWorkflowTools
License: Artistic-2.0
MD5sum: 5722e0caa8aff512c47588e418adc30c
NeedsCompilation: no
Title: BioC Workflow about publishing a Bioc Workflow
Description: Bioconductor Workflow describing how to use
        BiocWorkflowTools to work with a single R Markdown document to
        submit to both Bioconductor and F1000Research.
biocViews: BasicWorkflow
Author: Mike Smith [aut, cre], Andrzej OleÅ› [aut], Wolfgang Huber [ctb]
Maintainer: Mike Smith <grimbough@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/BiocMetaWorkflow
git_branch: RELEASE_3_20
git_last_commit: ee879cf
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/BiocMetaWorkflow_1.28.0.tar.gz
vignettes:
        vignettes/BiocMetaWorkflow/inst/doc/Authoring_BioC_Workflows.html
vignetteTitles: Bioc Meta Workflow
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BiocMetaWorkflow/inst/doc/Authoring_BioC_Workflows.R
dependencyCount: 0

Package: BP4RNAseq
Version: 1.16.0
Depends: R (>= 4.0.0)
Imports: dplyr, fastqcr, stringr, tidyr, stats, utils, magrittr,
        reticulate
Suggests: knitr, rmarkdown, testthat
License: GPL-2
MD5sum: fc0ab6f6eb3bee9458ec96cc4a04a53f
NeedsCompilation: no
Title: A babysitter's package for reproducible RNA-seq analysis
Description: An automated pipe for reproducible RNA-seq analysis with
        the minimal efforts from researchers. The package can process
        bulk RNA-seq data and single-cell RNA-seq data. You can only
        provide the taxa name and the accession id of RNA-seq data
        deposited in the National Center for Biotechnology Information
        (NCBI). After a cup of tea or longer, you will get formated
        gene expression data as gene count and transcript count based
        on both alignment-based and alignment-free workflows.
biocViews: GeneExpressionWorkflow
Author: Shanwen Sun [cre, aut], Lei Xu [aut], Quan Zou [aut]
Maintainer: Shanwen Sun <sunshanwen@gmail.com>
SystemRequirements: UNIX, SRA Toolkit=2.10.3, Entrez Direct=13.3,
        FastQC=v0.11.9, Cutadapt=2.10, datasets, SAMtools=1.9,
        HISAT2=2.2.0, StringTie=2.1.1, Salmon=1.2.1
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/BP4RNAseq
git_branch: RELEASE_3_20
git_last_commit: 64287a3
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/BP4RNAseq_1.16.0.tar.gz
vignettes: vignettes/BP4RNAseq/inst/doc/vignette.html
vignetteTitles: BP4RNAseq vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BP4RNAseq/inst/doc/vignette.R
dependencyCount: 91

Package: CAGEWorkflow
Version: 1.22.0
Depends: R (>= 3.6.0), CAGEfightR, nanotubes
Suggests: knitr, magick, rmarkdown, BiocStyle, BiocWorkflowTools,
        pheatmap, ggseqlogo, viridis, magrittr, ggforce, ggthemes,
        tidyverse, dplyr, GenomicRanges, SummarizedExperiment,
        GenomicFeatures, BiocParallel, InteractionSet, Gviz, DESeq2,
        limma, edgeR, statmod, BiasedUrn, sva, TFBSTools, motifmatchr,
        pathview, BSgenome.Mmusculus.UCSC.mm9,
        TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, JASPAR2016,
        png
License: GPL-3
MD5sum: 6058adc99103298e1b9ef4e39ddff52a
NeedsCompilation: no
Title: A step-by-step guide to analyzing CAGE data using R/Bioconductor
Description: Workflow for analyzing Cap Analysis of Gene Expression
        (CAGE) data using R/Bioconductor.
biocViews: GeneExpressionWorkflow, AnnotationWorkflow
Author: Malte Thodberg [aut, cre]
Maintainer: Malte Thodberg <maltethodberg@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CAGEWorkflow
git_branch: RELEASE_3_20
git_last_commit: 5c2322c
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/CAGEWorkflow_1.22.0.tar.gz
vignettes: vignettes/CAGEWorkflow/inst/doc/CAGEWorkflow.html
vignetteTitles: CAGEWorkflow
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CAGEWorkflow/inst/doc/CAGEWorkflow.R
dependencyCount: 166

Package: chipseqDB
Version: 1.30.0
Suggests: chipseqDBData, BiocStyle, BiocFileCache, ChIPpeakAnno, Gviz,
        Rsamtools, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR,
        knitr, org.Mm.eg.db, rtracklayer, rmarkdown
License: Artistic-2.0
MD5sum: 1d968a679efa162e9c2ab075e8dead18
NeedsCompilation: no
Title: A Bioconductor Workflow to Detect Differential Binding in
        ChIP-seq Data
Description: Describes a computational workflow for performing a DB
        analysis with sliding windows. The aim is to facilitate the
        practical implementation of window-based DB analyses by
        providing detailed code and expected output. The workflow
        described here applies to any ChIP-seq experiment with multiple
        experimental conditions and multiple biological samples in one
        or more of the conditions. It detects and summarizes DB regions
        between conditions in a de novo manner, i.e., without making
        any prior assumptions about the location or width of bound
        regions. Detected regions are then annotated according to their
        proximity to genes.
biocViews: ImmunoOncologyWorkflow, Workflow, EpigeneticsWorkflow
Author: Aaron Lun [aut, cre], Gordon Smyth [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
URL: https://www.bioconductor.org/help/workflows/chipseqDB/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/chipseqDB
git_branch: RELEASE_3_20
git_last_commit: fd8bc68
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/chipseqDB_1.30.0.tar.gz
vignettes: vignettes/chipseqDB/inst/doc/cbp.html,
        vignettes/chipseqDB/inst/doc/h3k27me3.html,
        vignettes/chipseqDB/inst/doc/h3k9ac.html,
        vignettes/chipseqDB/inst/doc/intro.html
vignetteTitles: 3. Differential binding of CBP in fibroblasts, 4.
        Differential enrichment of H3K27me3 in lung epithelium, 2.
        Differential enrichment of H3K9ac in B cells, 1. Introduction
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/chipseqDB/inst/doc/cbp.R
dependencyCount: 0

Package: csawUsersGuide
Version: 1.22.0
Suggests: knitr, BiocStyle, BiocManager
License: GPL-3
MD5sum: 9b846d5964a5bc954f83779afbffc996
NeedsCompilation: no
Title: csaw User's Guide
Description: A user's guide for the csaw package for detecting
        differentially bound regions in ChIP-seq data. Describes how to
        read in BAM files to obtain a per-window count matrix,
        filtering to obtain high-abundance windows of interest,
        normalization of sample-specific biases, testing for
        differential binding, consolidation of per-window results to
        obtain per-region statistics, and annotation and visualization
        of the DB results.
biocViews: Workflow, EpigeneticsWorkflow
Author: Aaron Lun [aut, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/csawUsersGuide
git_branch: RELEASE_3_20
git_last_commit: ee4d46c
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/csawUsersGuide_1.22.0.tar.gz
vignettes: vignettes/csawUsersGuide/inst/doc/csaw.pdf
vignetteTitles: User's guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/csawUsersGuide/inst/doc/csaw.R
dependencyCount: 0

Package: cytofWorkflow
Version: 1.30.0
Depends: R (>= 3.6.0), BiocStyle, knitr, readxl, CATALYST, diffcyt,
        HDCytoData, uwot, cowplot
Suggests: knitcitations, markdown, rmarkdown
License: Artistic-2.0
MD5sum: af9b23a8b9c85e044e2f08121fcae008
NeedsCompilation: no
Title: CyTOF workflow: differential discovery in high-throughput
        high-dimensional cytometry datasets
Description: High-dimensional mass and flow cytometry (HDCyto)
        experiments have become a method of choice for high-throughput
        interrogation and characterization of cell populations. Here,
        we present an updated R-based pipeline for differential
        analyses of HDCyto data, largely based on Bioconductor
        packages. We computationally define cell populations using
        FlowSOM clustering, and facilitate an optional but reproducible
        strategy for manual merging of algorithm-generated clusters.
        Our workflow offers different analysis paths, including
        association of cell type abundance with a phenotype or changes
        in signaling markers within specific subpopulations, or
        differential analyses of aggregated signals. Importantly, the
        differential analyses we show are based on regression
        frameworks where the HDCyto data is the response; thus, we are
        able to model arbitrary experimental designs, such as those
        with batch effects, paired designs and so on. In particular, we
        apply generalized linear mixed models or linear mixed models to
        analyses of cell population abundance or
        cell-population-specific analyses of signaling markers,
        allowing overdispersion in cell count or aggregated signals
        across samples to be appropriately modeled. To support the
        formal statistical analyses, we encourage exploratory data
        analysis at every step, including quality control (e.g.,
        multi-dimensional scaling plots), reporting of clustering
        results (dimensionality reduction, heatmaps with dendrograms)
        and differential analyses (e.g., plots of aggregated signals).
biocViews: ImmunoOncologyWorkflow, Workflow, SingleCellWorkflow
Author: Malgorzata Nowicka [aut], Helena L. Crowell [aut], Mark D.
        Robinson [aut, cre]
Maintainer: Mark D. Robinson <mark.robinson@mls.uzh.ch>
URL: https://github.com/markrobinsonuzh/cytofWorkflow
VignetteBuilder: knitr
BugReports: https://github.com/markrobinsonuzh/cytofWorkflow/issues
git_url: https://git.bioconductor.org/packages/cytofWorkflow
git_branch: RELEASE_3_20
git_last_commit: 39a5d29
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/cytofWorkflow_1.30.0.tar.gz
vignettes: vignettes/cytofWorkflow/inst/doc/cytofWorkflow.html
vignetteTitles: A workflow for differential discovery in
        high-throughput high-dimensional cytometry datasets
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 231

Package: EGSEA123
Version: 1.30.0
Depends: R (>= 3.4.0), EGSEA (>= 1.5.2), limma (>= 3.49.2), edgeR,
        illuminaio
Suggests: knitr, rmarkdown, BiocStyle
License: Artistic-2.0
MD5sum: a1ae6f35b2b72d549bdb5c52ee41e6d1
NeedsCompilation: no
Title: Easy and efficient ensemble gene set testing with EGSEA
Description: R package that supports the workflow article `Easy and
        efficient ensemble gene set testing with EGSEA', Alhamdoosh et
        al. (2017), F1000Research, 6:2010.
biocViews: ImmunoOncologyWorkflow, Workflow, GeneExpressionWorkflow
Author: Monther Alhamdoosh, Charity Law, Luyi Tian, Julie Sheridan,
        Milica Ng and Matthew Ritchie
Maintainer: Matthew Ritchie <mritchie@wehi.edu.au>
URL: https://f1000research.com/articles/6-2010
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/EGSEA123
git_branch: RELEASE_3_20
git_last_commit: bb5a27e
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/EGSEA123_1.30.0.tar.gz
vignettes: vignettes/EGSEA123/inst/doc/EGSEAWorkflow.html
vignetteTitles: Easy and efficient ensemble gene set testing with EGSEA
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/EGSEA123/inst/doc/EGSEAWorkflow.R
dependencyCount: 203

Package: ExpHunterSuite
Version: 1.14.0
Depends: R (>= 4.1.0)
Imports: ReactomePA, limma, edgeR, NOISeq, biomaRt, topGO, diffcoexp,
        DT, ggplot2, stringr, WGCNA, dplyr, AnnotationDbi,
        BiocGenerics, enrichplot, rmarkdown, stats, Biobase, DESeq2,
        ROCR, data.table, knitr, magrittr, SummarizedExperiment,
        miRBaseVersions.db, grDevices, graphics, utils, BiocParallel,
        MKinfer, matrixStats, ggupset, rlang, plyr, tidyr, GO.db,
        Matrix, fastcluster, DOSE, heatmaply, EnhancedVolcano, ggrepel,
        clusterProfiler, GenomicRanges, GenomicFeatures, tximport,
        annotatr, ggridges, FactoInvestigate, FactoMineR
Suggests: optparse, PerformanceAnalytics, naivebayes, reshape2,
        org.Hs.eg.db, org.Mm.eg.db, testthat (>= 3.0.0)
License: MIT + file LICENSE
MD5sum: 8b6801c707b0c09025497440976d8c00
NeedsCompilation: no
Title: Package For The Comprehensive Analysis Of Transcriptomic Data
Description: The ExpHunterSuite implements a comprehensive protocol for
        the analysis of transcriptional data using established *R*
        packages and combining their results. It covers all key steps
        in DEG detection, CEG detection and functional analysis for
        RNA-seq data. It has been implemented as an R package
        containing functions that can be run interactively. In
        addition, it also contains scripts that wrap the functions and
        can be run directly from the command line.
biocViews: GeneExpressionWorkflow
Author: James Perkins [aut, cre]
        (<https://orcid.org/0000-0003-4108-096X>), Pedro Seoane Zonjic
        [aut] (<https://orcid.org/0000-0002-3020-1415>), Fernando
        Moreno Jabato [aut] (<https://orcid.org/0000-0001-7498-1962>),
        José Córdoba Caballero [aut]
        (<https://orcid.org/0000-0002-1821-5742>), Elena Rojano Rivera
        [aut] (<https://orcid.org/0000-0002-2678-710X>), Rocio Bautista
        Moreno [aut] (<https://orcid.org/0000-0003-1685-8119>), M.
        Gonzalo Claros [aut] (<https://orcid.org/0000-0002-0112-3550>),
        Isabel Gonzalez Gayte [aut], Juan Antonio García Ranea [aut]
        (<https://orcid.org/0000-0003-0327-1837>)
Maintainer: James Perkins <jimrperkins@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ExpHunterSuite
git_branch: RELEASE_3_20
git_last_commit: bee5918
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/ExpHunterSuite_1.14.0.tar.gz
vignettes: vignettes/ExpHunterSuite/inst/doc/hunter.html
vignetteTitles: The Expression Hunter Suite
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/ExpHunterSuite/inst/doc/hunter.R
dependencyCount: 300

Package: ExpressionNormalizationWorkflow
Version: 1.32.0
Imports: Biobase (>= 2.24.0), limma (>= 3.20.9), lme4 (>= 1.1.7),
        matrixStats (>= 0.10.3), pvca (>= 1.4.0), snm (>= 1.12.0), sva
        (>= 3.10.0), vsn (>= 3.32.0)
Suggests: knitr, BiocStyle
License: GPL (>=3)
MD5sum: 9ae688ba3a55e9499c1463b535dbadde
NeedsCompilation: no
Title: Gene Expression Normalization Workflow
Description: An extensive, customized expression normalization workflow
        incorporating Supervised Normalization of Microarryas(SNM),
        Surrogate Variable Analysis(SVA) and Principal Variance
        Component Analysis to identify batch effects and remove them
        from the expression data to enhance the ability to detect the
        underlying biological signals.
biocViews: ImmunoOncologyWorkflow, Workflow, GeneExpressionWorkflow
Author: Karthikeyan Murugesan [aut, cre], Greg Gibson [sad, ths]
Maintainer: Karthikeyan Murugesan <karthikeyanm60@yahoo.com>
VignetteBuilder: knitr
BugReports: https://github.com/
git_url:
        https://git.bioconductor.org/packages/ExpressionNormalizationWorkflow
git_branch: RELEASE_3_20
git_last_commit: 2f5f1e6
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/ExpressionNormalizationWorkflow_1.32.0.tar.gz
vignettes:
        vignettes/ExpressionNormalizationWorkflow/inst/doc/genExpNrm.html
vignetteTitles: Gene Expression Normalization Workflow
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ExpressionNormalizationWorkflow/inst/doc/genExpNrm.R
dependencyCount: 106

Package: fluentGenomics
Version: 1.18.0
Depends: R (>= 4.0)
Imports: plyranges (>= 1.7.7), dplyr, SummarizedExperiment, readr,
        stats, utils
Suggests: knitr, rmarkdown, bookdown, rappdirs, BiocFileCache, DESeq2,
        limma, ggplot2, tidyr, tximeta (>= 1.4.2), macrophage (>=
        1.2.0),
License: MIT + file LICENSE
MD5sum: 8b1094d60ef003502ec90ac51b269460
NeedsCompilation: no
Title: A plyranges and tximeta workflow
Description: An extended workflow using the plyranges and tximeta
        packages for fluent genomic data analysis. Use tximeta to
        correctly import RNA-seq transcript quantifications and
        summarize them to gene counts for downstream analysis. Use
        plyranges for clearly expressing operations over genomic
        coordinates and to combine results from differential expression
        and differential accessibility analyses.
biocViews: Workflow, BasicWorkflow, GeneExpressionWorkflow
Author: Stuart Lee [aut, cre]
        (<https://orcid.org/0000-0003-1179-8436>), Michael Love [aut,
        ctb]
Maintainer: Stuart Lee <stuart.andrew.lee@gmail.com>
URL: https://github.com/sa-lee/fluentGenomics
VignetteBuilder: knitr, rmarkdown
BugReports: https://github.com/sa-lee/fluentGenomics/issues
git_url: https://git.bioconductor.org/packages/fluentGenomics
git_branch: RELEASE_3_20
git_last_commit: 51c0b4f
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/fluentGenomics_1.18.0.tar.gz
vignettes: vignettes/fluentGenomics/inst/doc/fluentGenomics.html
vignetteTitles: fluentGenomics
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/fluentGenomics/inst/doc/fluentGenomics.R
dependencyCount: 83

Package: generegulation
Version: 1.30.0
Depends: R (>= 3.3.0), BSgenome.Scerevisiae.UCSC.sacCer3, Biostrings,
        GenomicFeatures, MotifDb, S4Vectors,
        TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, motifStack,
        org.Sc.sgd.db, seqLogo
Suggests: knitr, rmarkdown, BiocStyle
License: Artistic-2.0
MD5sum: f082cf8d381558804023a760c5e59dca
NeedsCompilation: no
Title: Finding Candidate Binding Sites for Known Transcription Factors
        via Sequence Matching
Description: The binding of transcription factor proteins (TFs) to DNA
        promoter regions upstream of gene transcription start sites
        (TSSs) is one of the most important mechanisms by which gene
        expression, and thus many cellular processes, are controlled.
        Though in recent years many new kinds of data have become
        available for identifying transcription factor binding sites
        (TFBSs) -- ChIP-seq and DNase I hypersensitivity regions among
        them -- sequence matching continues to play an important role.
        In this workflow we demonstrate Bioconductor techniques for
        finding candidate TF binding sites in DNA sequence using the
        model organism Saccharomyces cerevisiae.  The methods
        demonstrated here apply equally well to other organisms.
biocViews: Workflow, EpigeneticsWorkflow
Author: Bioconductor Package Maintainer [aut, cre]
Maintainer: Bioconductor Package Maintainer
        <maintainer@bioconductor.org>
URL: https://www.bioconductor.org/help/workflows/generegulation/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/generegulation
git_branch: RELEASE_3_20
git_last_commit: 46eab17
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/generegulation_1.30.0.tar.gz
vignettes: vignettes/generegulation/inst/doc/generegulation.html
vignetteTitles: Finding Candidate Binding Sites for Known Transcription
        Factors via Sequence Matching
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/generegulation/inst/doc/generegulation.R
dependencyCount: 154

Package: GeoMxWorkflows
Version: 1.12.0
Depends: R (>= 4.0), NanoStringNCTools, GeomxTools
Imports: Biobase, S4Vectors, rjson, readxl, EnvStats, dplyr, reshape2,
        methods, utils, stats, data.table, outliers, BiocGenerics,
        ggplot2, ggrepel, ggforce, cowplot, scales, umap, Rtsne,
        pheatmap, BiocStyle, networkD3
Suggests: rmarkdown, knitr
License: MIT
MD5sum: 9ced66d7091146c958b3a0dbbd71ac5e
NeedsCompilation: no
Title: GeoMx Digital Spatial Profiler (DSP) data analysis workflows
Description: Workflows for use with NanoString Technologies GeoMx
        Technology.  Package provides bioconductor focused workflows
        for leveraging existing packages (e.g. GeomxTools) to process,
        QC, and analyze the data.
biocViews: GeneExpressionWorkflow, ImmunoOncologyWorkflow,
        SpatialWorkflow
Author: Maddy Griswold [cre, aut], Jason Reeves [aut], Prajan Divakar
        [aut], Nicole Ortogero [aut], Zhi Yang [aut], Stephanie
        Zimmerman [aut], Rona Vitancol [aut], David Henderson [aut]
Maintainer: Maddy Griswold <mgriswold@nanostring.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GeoMxWorkflows
git_branch: RELEASE_3_20
git_last_commit: ca39c86
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/GeoMxWorkflows_1.12.0.tar.gz
vignettes:
        vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html
vignetteTitles: Analyzing GeoMx-NGS Data with GeomxTools
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.R
dependencyCount: 151

Package: highthroughputassays
Version: 1.30.0
Depends: R (>= 3.3.0), flowCore, flowStats, flowWorkspace
Suggests: knitr, rmarkdown, BiocStyle
License: Artistic-2.0
MD5sum: b5754024a9ecb7e6103aa2316da75a97
NeedsCompilation: no
Title: Using Bioconductor with High Throughput Assays
Description: The workflow illustrates use of the flow cytometry
        packages to load, transform and visualize the flow data and
        gate certain populations in the dataset. The workflow loads the
        `flowCore`, `flowStats` and `flowWorkspace` packages and its
        dependencies.  It loads the ITN data with 15 samples, each of
        which includes, in addition to FSC and SSC, 5 fluorescence
        channels: CD3, CD4, CD8, CD69 and HLADR.
biocViews: ImmunoOncologyWorkflow, Workflow, ProteomicsWorkflow
Author: Bioconductor Package Maintainer [aut, cre]
Maintainer: Bioconductor Package Maintainer
        <maintainer@bioconductor.org>
URL: https://www.bioconductor.org/help/workflows/highthroughputassays/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/highthroughputassays
git_branch: RELEASE_3_20
git_last_commit: 45c7bdc
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/highthroughputassays_1.30.0.tar.gz
vignettes:
        vignettes/highthroughputassays/inst/doc/high-throughput-assays.html
vignetteTitles: Using Bioconductor with High Throughput Assays
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
        vignettes/highthroughputassays/inst/doc/high-throughput-assays.R
dependencyCount: 102

Package: liftOver
Version: 1.30.0
Depends: R (>= 3.3.0), gwascat, GenomicRanges, rtracklayer,
        Homo.sapiens, BiocGenerics
Suggests: knitr, rmarkdown, BiocStyle
License: Artistic-2.0
MD5sum: 96d602fc58cadb59cbe5dd334d60d72c
NeedsCompilation: no
Title: Changing genomic coordinate systems with rtracklayer::liftOver
Description: The liftOver facilities developed in conjunction with the
        UCSC browser track infrastructure are available for
        transforming data in GRanges formats.  This is illustrated here
        with an image of the EBI/NHGRI GWAS catalog that is, as of May
        10 2017, distributed with coordinates defined by NCBI build
        hg38.
biocViews: Workflow, BasicWorkflow
Author: Bioconductor Package Maintainer [aut, cre]
Maintainer: Bioconductor Package Maintainer
        <maintainer@bioconductor.org>
URL: https://www.bioconductor.org/help/workflows/liftOver/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/liftOver
git_branch: RELEASE_3_20
git_last_commit: abb006b
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/liftOver_1.30.0.tar.gz
vignettes: vignettes/liftOver/inst/doc/liftov.html
vignetteTitles: Changing genomic coordinate systems with
        rtracklayer::liftOver
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/liftOver/inst/doc/liftov.R
dependencyCount: 122

Package: maEndToEnd
Version: 2.26.0
Depends: R (>= 3.5.0), Biobase, oligoClasses, ArrayExpress,
        pd.hugene.1.0.st.v1, hugene10sttranscriptcluster.db, oligo,
        arrayQualityMetrics, limma, topGO, ReactomePA, clusterProfiler,
        gplots, ggplot2, geneplotter, pheatmap, RColorBrewer, dplyr,
        tidyr, stringr, matrixStats, genefilter, openxlsx, Rgraphviz,
        enrichplot
Suggests: BiocStyle, knitr, devtools, rmarkdown
License: MIT + file LICENSE
MD5sum: c95804388a19f03292ecd607fae9060c
NeedsCompilation: no
Title: An end to end workflow for differential gene expression using
        Affymetrix microarrays
Description: In this article, we walk through an end-to-end Affymetrix
        microarray differential expression workflow using Bioconductor
        packages. This workflow is directly applicable to current
        "Gene" type arrays, e.g. the HuGene or MoGene arrays, but can
        easily be adapted to similar platforms. The data analyzed here
        is a typical clinical microarray data set that compares
        inflamed and non-inflamed colon tissue in two disease subtypes.
        For each disease, the differential gene expression between
        inflamed- and non-inflamed colon tissue was analyzed. We will
        start from the raw data CEL files, show how to import them into
        a Bioconductor ExpressionSet, perform quality control and
        normalization and finally differential gene expression (DE)
        analysis, followed by some enrichment analysis.
biocViews: GeneExpressionWorkflow
Author: Bernd Klaus [aut], Stefanie Reisenauer [aut, cre]
Maintainer: Stefanie Reisenauer <steffi.reisenauer@tum.de>
URL: https://www.bioconductor.org/help/workflows/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/maEndToEnd
git_branch: RELEASE_3_20
git_last_commit: 69484ff
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/maEndToEnd_2.26.0.tar.gz
vignettes: vignettes/maEndToEnd/inst/doc/MA-Workflow.html
vignetteTitles: An end to end workflow for differential gene expression
        using Affymetrix microarrays
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/maEndToEnd/inst/doc/MA-Workflow.R
dependencyCount: 217

Package: methylationArrayAnalysis
Version: 1.29.0
Depends: R (>= 3.3.0), knitr, rmarkdown, BiocStyle, limma, minfi,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylation450kmanifest, RColorBrewer, missMethyl,
        matrixStats, minfiData, Gviz, DMRcate, stringr,
        FlowSorted.Blood.450k
License: Artistic-2.0
MD5sum: 502cab1033c9ccf24bee83d698470f57
NeedsCompilation: no
Title: A cross-package Bioconductor workflow for analysing methylation
        array data.
Description: Methylation in the human genome is known to be associated
        with development and disease. The Illumina Infinium methylation
        arrays are by far the most common way to interrogate
        methylation across the human genome. This Bioconductor workflow
        uses multiple packages for the analysis of methylation array
        data. Specifically, we demonstrate the steps involved in a
        typical differential methylation analysis pipeline including:
        quality control, filtering, normalization, data exploration and
        statistical testing for probe-wise differential methylation. We
        further outline other analyses such as differential methylation
        of regions, differential variability analysis, estimating cell
        type composition and gene ontology testing. Finally, we provide
        some examples of how to visualise methylation array data.
biocViews: Workflow, EpigeneticsWorkflow
Author: Jovana Maksimovic [aut, cre]
Maintainer: Jovana Maksimovic <jovana.maksimovic@mcri.edu.au>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/methylationArrayAnalysis
git_branch: devel
git_last_commit: a9a1a87
git_last_commit_date: 2024-04-30
Date/Publication: 2024-04-30
source.ver: src/contrib/methylationArrayAnalysis_1.29.0.tar.gz
vignettes:
        vignettes/methylationArrayAnalysis/inst/doc/methylationArrayAnalysis.html
vignetteTitles: A cross-package Bioconductor workflow for analysing
        methylation array data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
        vignettes/methylationArrayAnalysis/inst/doc/methylationArrayAnalysis.R
dependencyCount: 229

Package: recountWorkflow
Version: 1.30.0
Depends: R (>= 3.6.0)
Imports: recount, GenomicRanges, limma, edgeR, DESeq2, pheatmap,
        regionReport, clusterProfiler, org.Hs.eg.db, gplots, derfinder,
        GenomicState, bumphunter, derfinderPlot
Suggests: BiocStyle, BiocWorkflowTools, knitr, magick, sessioninfo,
        rmarkdown
License: Artistic-2.0
MD5sum: 96d559d5b68ec31262af510700600681
NeedsCompilation: no
Title: recount workflow: accessing over 70,000 human RNA-seq samples
        with Bioconductor
Description: The recount2 resource is composed of over 70,000 uniformly
        processed human RNA-seq samples spanning TCGA and SRA,
        including GTEx. The processed data can be accessed via the
        recount2 website and the recount Bioconductor package. This
        workflow explains in detail how to use the recount package and
        how to integrate it with other Bioconductor packages for
        several analyses that can be carried out with the recount2
        resource. In particular, we describe how the coverage count
        matrices were computed in recount2 as well as different ways of
        obtaining public metadata, which can facilitate downstream
        analyses. Step-by-step directions show how to do a gene level
        differential expression analysis, visualize base-level genome
        coverage data, and perform an analyses at multiple feature
        levels. This workflow thus provides further information to
        understand the data in recount2 and a compendium of R code to
        use the data.
biocViews: Workflow, ResourceQueryingWorkflow
Author: Leonardo Collado-Torres [aut, cre], Abhinav Nellore [ctb],
        Andrew E. Jaffe [ctb]
Maintainer: Leonardo Collado-Torres <lcolladotor@gmail.com>
URL: https://github.com/LieberInstitute/recountWorkflow
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/t/recountWorkflow/
git_url: https://git.bioconductor.org/packages/recountWorkflow
git_branch: RELEASE_3_20
git_last_commit: 71c82c8
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/recountWorkflow_1.30.0.tar.gz
vignettes: vignettes/recountWorkflow/inst/doc/recount-workflow.html
vignetteTitles: recount workflow: accessing over 70,,000 human RNA-seq
        samples with Bioconductor
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/recountWorkflow/inst/doc/recount-workflow.R
dependencyCount: 240

Package: RNAseq123
Version: 1.30.0
Depends: R (>= 3.3.0), Glimma (>= 1.1.9), limma, edgeR, gplots,
        RColorBrewer, Mus.musculus, R.utils, TeachingDemos, statmod,
        BiocWorkflowTools
Suggests: knitr, rmarkdown, BiocStyle
License: Artistic-2.0
MD5sum: 8e89b0fb49b37097ad3ec0383134ea3e
NeedsCompilation: no
Title: RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Description: R package that supports the F1000Research workflow article
        on RNA-seq analysis using limma, Glimma and edgeR by Law et al.
        (2016).
biocViews: Workflow, GeneExpressionWorkflow, ImmunoOncologyWorkflow
Author: Charity Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi
        Tian, Gordon Smyth and Matthew Ritchie
Maintainer: Matthew Ritchie <mritchie@wehi.edu.au>
URL: https://f1000research.com/articles/5-1408/v3
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RNAseq123
git_branch: RELEASE_3_20
git_last_commit: 519935d
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/RNAseq123_1.30.0.tar.gz
vignettes: vignettes/RNAseq123/inst/doc/designmatrices.html,
        vignettes/RNAseq123/inst/doc/limmaWorkflow_CHN.html,
        vignettes/RNAseq123/inst/doc/limmaWorkflow.html
vignetteTitles: A guide to creating design matrices for gene expression
        experiments (English version), RNA-seq analysis is easy as
        1-2-3 with limma,, Glimma and edgeR (Chinese version), RNA-seq
        analysis is easy as 1-2-3 with limma,, Glimma and edgeR
        (English version)
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RNAseq123/inst/doc/designmatrices.R,
        vignettes/RNAseq123/inst/doc/limmaWorkflow_CHN.R,
        vignettes/RNAseq123/inst/doc/limmaWorkflow.R
dependencyCount: 170

Package: rnaseqDTU
Version: 1.26.0
Depends: R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib,
        devtools
Suggests: knitr, rmarkdown
License: Artistic-2.0
MD5sum: 39e3d826423ab2cb9454c78f86ac4c72
NeedsCompilation: no
Title: RNA-seq workflow for differential transcript usage following
        Salmon quantification
Description: RNA-seq workflow for differential transcript usage (DTU)
        following Salmon quantification. This workflow uses
        Bioconductor packages tximport, DRIMSeq, and DEXSeq to perform
        a DTU analysis on simulated data. It also shows how to use
        stageR to perform two-stage testing of DTU, a statistical
        framework to screen at the gene level and then confirm which
        transcripts within the significant genes show evidence of DTU.
biocViews: Workflow, GeneExpressionWorkflow, ImmunoOncologyWorkflow
Author: Michael Love [aut, cre], Charlotte Soneson [aut], Rob Patro
        [aut]
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
URL: https://github.com/thelovelab/rnaseqDTU/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/rnaseqDTU
git_branch: RELEASE_3_20
git_last_commit: a4bd01b
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/rnaseqDTU_1.26.0.tar.gz
vignettes: vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html
vignetteTitles: RNA-seq workflow for differential transcript usage
        following Salmon quantification
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rnaseqDTU/inst/doc/rnaseqDTU.R
dependencyCount: 186

Package: rnaseqGene
Version: 1.30.0
Depends: R (>= 3.3.0), BiocStyle, airway (>= 1.5.3), tximeta, magrittr,
        DESeq2, apeglm, vsn, dplyr, ggplot2, hexbin, pheatmap,
        RColorBrewer, PoiClaClu, glmpca, ggbeeswarm, genefilter,
        AnnotationDbi, org.Hs.eg.db, Gviz, sva, RUVSeq, fission
Suggests: knitr, rmarkdown
License: Artistic-2.0
MD5sum: 2a3e5ba7a278064ef25286fd8b03706d
NeedsCompilation: no
Title: RNA-seq workflow: gene-level exploratory analysis and
        differential expression
Description: Here we walk through an end-to-end gene-level RNA-seq
        differential expression workflow using Bioconductor packages.
        We will start from the FASTQ files, show how these were aligned
        to the reference genome, and prepare a count matrix which
        tallies the number of RNA-seq reads/fragments within each gene
        for each sample.  We will perform exploratory data analysis
        (EDA) for quality assessment and to explore the relationship
        between samples, perform differential gene expression analysis,
        and visually explore the results.
biocViews: Workflow, GeneExpressionWorkflow, ImmunoOncologyWorkflow
Author: Michael Love [aut, cre]
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
URL: https://github.com/thelovelab/rnaseqGene/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/rnaseqGene
git_branch: RELEASE_3_20
git_last_commit: cf0c3fd
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/rnaseqGene_1.30.0.tar.gz
vignettes: vignettes/rnaseqGene/inst/doc/rnaseqGene.html
vignetteTitles: RNA-seq workflow at the gene level
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rnaseqGene/inst/doc/rnaseqGene.R
dependencyCount: 208

Package: RnaSeqGeneEdgeRQL
Version: 1.30.0
Depends: R (>= 3.3.0), edgeR (>= 4.3.6), gplots, org.Mm.eg.db, GO.db,
        BiocStyle
Suggests: knitr, knitcitations, rmarkdown
License: Artistic-2.0
MD5sum: 3c8cf4739e5e804c2b8b8b9aa3f82c2c
NeedsCompilation: no
Title: Gene-level RNA-seq differential expression and pathway analysis
        using Rsubread and the edgeR quasi-likelihood pipeline
Description: This workflow package provides, through its vignette, a
        complete case study analysis of an RNA-Seq experiment using the
        Rsubread and edgeR packages. The workflow starts from read
        alignment and continues on to data exploration, to differential
        expression and, finally, to pathway analysis. The analysis
        includes publication quality plots, GO and KEGG analyses, and
        the analysis of a expression signature as generated by a prior
        experiment.
biocViews: Workflow, GeneExpressionWorkflow, ImmunoOncologyWorkflow
Author: Yunshun Chen, Aaron Lun, Gordon Smyth
Maintainer: Yunshun Chen <yuchen@wehi.edu.au>
URL: http://f1000research.com/articles/5-1438/v2
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RnaSeqGeneEdgeRQL
git_branch: RELEASE_3_20
git_last_commit: 1be8f2e
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/RnaSeqGeneEdgeRQL_1.30.0.tar.gz
vignettes: vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.html
vignetteTitles: From reads to genes to pathways: differential
        expression analysis of RNA-Seq experiments using Rsubread and
        the edgeR quasi-likelihood pipeline
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.R
dependencyCount: 77

Package: seqpac
Version: 1.6.0
Depends: R (>= 4.2.0)
Imports: Biostrings (>= 2.46.0), foreach (>= 1.5.1), GenomicRanges (>=
        1.30.3), Rbowtie (>= 1.18.0), ShortRead (>= 1.36.1), tibble (>=
        3.1.2), BiocParallel (>= 1.12.0), cowplot (>= 0.9.4),
        data.table (>= 1.14.0), digest (>= 0.6.27), doParallel (>=
        1.0.16), dplyr (>= 1.0.6), factoextra (>= 1.0.7), FactoMineR
        (>= 1.41), ggplot2 (>= 3.3.3), IRanges (>= 2.12.0), parallel
        (>= 3.4.4), reshape2 (>= 1.4.4), rtracklayer (>= 1.38.3),
        stringr (>= 1.4.0), stats (>= 3.4.4), methods, S4Vectors
Suggests: benchmarkme (>= 0.6.0), DESeq2 (>= 1.18.1), GenomeInfoDb (>=
        1.14.0), gginnards (>= 0.0.2), qqman (>= 0.1.8), rmarkdown,
        BiocStyle, knitr, testthat, UpSetR (>= 1.4.0), venneuler,
        R.utils, bigreadr, readr, vroom
License: GPL-3
MD5sum: 1b47a108989e9a510609e8cda4236a9a
NeedsCompilation: no
Title: Seqpac: A Framework for smallRNA analysis in R using
        Sequence-Based Counts
Description: Seqpac provides functions and workflows for analysis of
        short sequenced reads. It was originally developed for small
        RNA analysis, but can be implemented on any sequencing raw data
        (provided as a fastq-file), where the unit of measurement is
        counts of unique sequences. The core of the seqpac workflow is
        the generation and subsequence analysis/visualization of a
        standardized object called PAC. Using an innovative targeting
        system, Seqpac process, analyze and visualize sample or
        sequence group differences using the PAC object. A PAC object
        in its most basic form is a list containing three types of data
        frames. - Phenotype table (P): Sample names (rows) with
        associated metadata (columns) e.g. treatment. - Annotation
        table (A): Unique sequences (rows) with annotation (columns),
        eg. reference alignments. - Counts table (C): Counts of unique
        sequences (rows) for each sample (columns). The PAC-object
        follows the rule: - Row names in P must be identical with
        column names in C. - Row names in A must be identical with row
        names in C. Thus P and A describes the columns and rows in C,
        respectively. The targeting system, will either target specific
        samples in P (pheno_target) or sequences in A (anno_target) and
        group them according to a target column in P and A,
        respectively (see vignettes for more details).
biocViews: Workflow, BasicWorkflow, GeneExpressionWorkflow,
        EpigeneticsWorkflow, AnnotationWorkflow
Author: Daniel Natt [aut, cre, fnd], Lovisa Örkenby [ctb], Signe Skog
        [ctb], Anita Öst [aut, fnd]
Maintainer: Daniel Natt <daniel.natt@liu.se>
URL: https://github.com/Danis102/seqpac
VignetteBuilder: knitr
BugReports: https://github.com/Danis102/seqpac/issues
git_url: https://git.bioconductor.org/packages/seqpac
git_branch: RELEASE_3_20
git_last_commit: 7c56287
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/seqpac_1.6.0.tar.gz
vignettes:
        vignettes/seqpac/inst/doc/seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.html
vignetteTitles: A guide to small RNA analysis using Seqpac
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
        vignettes/seqpac/inst/doc/seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.R
dependencyCount: 179

Package: sequencing
Version: 1.30.0
Depends: R (>= 3.3.0), GenomicRanges, GenomicAlignments, Biostrings,
        Rsamtools, ShortRead, BiocParallel, rtracklayer,
        VariantAnnotation, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
        RNAseqData.HNRNPC.bam.chr14
Suggests: knitr, rmarkdown, BiocStyle
License: Artistic-2.0
MD5sum: 556e5944a6f89d18d6e16980763a68bc
NeedsCompilation: no
Title: Introduction to Bioconductor for Sequence Data
Description: Bioconductor enables the analysis and comprehension of
        high- throughput genomic data. We have a vast number of
        packages that allow rigorous statistical analysis of large data
        while keeping technological artifacts in mind. Bioconductor
        helps users place their analytic results into biological
        context, with rich opportunities for visualization.
        Reproducibility is an important goal in Bioconductor analyses.
        Different types of analysis can be carried out using
        Bioconductor, for example; Sequencing : RNASeq, ChIPSeq,
        variants, copy number etc.; Microarrays: expression, SNP, etc.;
        Domain specific analysis : Flow cytometry, Proteomics etc. For
        these analyses, one typically imports and works with diverse
        sequence-related file types, including fasta, fastq, BAM, gtf,
        bed, and wig files, among others. Bioconductor packages support
        import, common and advanced sequence manipulation operations
        such as trimming, transformation, and alignment including
        quality assessment.
biocViews: ImmunoOncologyWorkflow, Workflow, BasicWorkflow
Author: Sonali Arora [aut], Martin Morgan [aut], Bioconductor Package
        Maintainer [cre]
Maintainer: Bioconductor Package Maintainer
        <maintainer@bioconductor.org>
URL: https://www.bioconductor.org/help/workflows/sequencing/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/sequencing
git_branch: RELEASE_3_20
git_last_commit: 0590f66
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/sequencing_1.30.0.tar.gz
vignettes: vignettes/sequencing/inst/doc/sequencing.html
vignetteTitles: Introduction to Bioconductor for Sequence Data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/sequencing/inst/doc/sequencing.R
dependencyCount: 112

Package: simpleSingleCell
Version: 1.30.0
Imports: utils, methods, knitr, callr, rmarkdown, CodeDepends,
        BiocStyle
Suggests: readxl, R.utils, SingleCellExperiment, scater, scran, limma,
        BiocFileCache, org.Mm.eg.db
License: Artistic-2.0
MD5sum: dba47b42f3e3b03cb1698e3edcb14cdb
NeedsCompilation: no
Title: A step-by-step workflow for low-level analysis of single-cell
        RNA-seq data with Bioconductor
Description: Once a proud workflow package, this is now a shell of its
        former self. Almost all of its content has been cannibalized
        for use in the "Orchestrating Single-Cell Analyses with
        Bioconductor" book at https://osca.bioconductor.org. Most
        vignettes here are retained as reminders of the glory that once
        was, also providing redirection for existing external links to
        the relevant OSCA book chapters.
biocViews: ImmunoOncologyWorkflow, Workflow, SingleCellWorkflow
Author: Aaron Lun [aut, cre], Davis McCarthy [aut], John Marioni [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
URL: https://www.bioconductor.org/help/workflows/simpleSingleCell/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/simpleSingleCell
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git_last_commit: d4956ae
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/simpleSingleCell_1.30.0.tar.gz
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vignetteTitles: 05. Correcting batch effects, 12. Scalability for big
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        Read count data, 07. Spike-in normalization, 04. Droplet-based
        data, 03. UMI count data, 09. Advanced variance modelling
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Package: SingscoreAMLMutations
Version: 1.22.0
Depends: R (>= 4.1.0)
Imports: dcanr, edgeR, ggplot2, gridExtra, GSEABase, mclust,
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Suggests: knitr, rmarkdown, BiocStyle, BiocWorkflowTools, spelling
License: Artistic-2.0
MD5sum: 68332c4b81d946273b740adab62d7a07
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Title: Using singscore to predict mutations in AML from transcriptomic
        signatures
Description: This workflow package shows how transcriptomic signatures
        can be used to infer phenotypes. The workflow begins by showing
        how the TCGA AML transcriptomic data can be downloaded and
        processed using the TCGAbiolinks packages. It then shows how
        samples can be scored using the singscore package and
        signatures from the MSigDB. Finally, the predictive capacity of
        scores in the context of predicting a specific mutation in AML
        is shown.The workflow exhibits the interplay of Bioconductor
        packages to achieve a gene-set level analysis.
biocViews: GeneExpressionWorkflow, GenomicVariantsWorkflow,
        ImmunoOncologyWorkflow, Workflow
Author: Dharmesh D. Bhuva [aut, cre]
        (<https://orcid.org/0000-0002-6398-9157>), Momeneh Foroutan
        [aut] (<https://orcid.org/0000-0002-1440-0457>), Yi Xie [aut]
        (<https://orcid.org/0000-0002-1938-4089>), Ruqian Lyu [aut],
        Malvika Kharbanda [aut]
        (<https://orcid.org/0000-0001-9726-3023>), Joseph Cursons [aut]
        (<https://orcid.org/0000-0002-5053-4540>), Melissa J. Davis
        [aut] (<https://orcid.org/0000-0003-4864-7033>)
Maintainer: Dharmesh D. Bhuva <bhuva.d@wehi.edu.au>
URL: https://github.com/DavisLaboratory/SingscoreAMLMutations
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BugReports:
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git_url: https://git.bioconductor.org/packages/SingscoreAMLMutations
git_branch: RELEASE_3_20
git_last_commit: 6384720
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/SingscoreAMLMutations_1.22.0.tar.gz
vignettes:
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vignetteTitles: Using singscore to predict mutations in AML from
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        predict mutations in AML from transcriptomic signatures
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dependencyCount: 172

Package: spicyWorkflow
Version: 1.6.0
Depends: R (>= 4.3.0)
Suggests: knitr, rmarkdown, BiocStyle, EBImage, cytomapper, ggplot2,
        ggpubr, lisaClust, spicyR, ClassifyR, scater, dplyr, simpleSeg,
        FuseSOM, HDF5Array, parallel, tidySingleCellExperiment,
        SpatialDatasets, Statial, treekoR
License: GPL-3
MD5sum: a5d38b9c5dd15d9a5048b853a27086ff
NeedsCompilation: no
Title: Performing a Spatial Analysis of Multiplexed Tissue Imaging Data
Description: We have developed an analytical framework for analysing
        data from high dimensional in situ cytometry assays including
        CODEX, CycIF, IMC and High Definition Spatial Transcriptomics.
        This framework makes use of functionality from our Bioconductor
        packages spicyR, lisaClust, scFeatures, FuseSOM, simpleSeg and
        ClassifyR and contains most of the key steps which are needed
        to interrogate the comprehensive spatial information generated
        by these exciting new technologies including cell segmentation,
        feature normalisation, cell type identification,
        micro-environment characterisation, spatial hypothesis testing
        and patient classification. Ultimately, our modular analysis
        framework provides a cohesive and accessible entry point into
        spatially resolved single cell data analysis for any R-based
        bioinformatician.
biocViews: Workflow, SpatialWorkflow, ImmunoOncologyWorkflow
Author: Alex Qin [aut], Alexander Nicholls [aut], Nicholas Robertson
        [aut], Nicolas Canete [aut], Elijah Willie [aut], Ellis Patrick
        [aut] (<https://orcid.org/0000-0002-5253-4747>), SOMS
        Maintainer [aut, cre]
Maintainer: SOMS Maintainer <maths.bioconductor@sydney.edu.au>
URL: https://github.com/SydneyBioX/spicyWorkflow
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BugReports: https://github.com/SydneyBioX/spicyWorkflow/issues
git_url: https://git.bioconductor.org/packages/spicyWorkflow
git_branch: RELEASE_3_20
git_last_commit: 74e88c5
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/spicyWorkflow_1.6.0.tar.gz
vignettes: vignettes/spicyWorkflow/inst/doc/spicyWorkflow.html
vignetteTitles: "Introduction to a spicy workflow"
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Rfiles: vignettes/spicyWorkflow/inst/doc/spicyWorkflow.R
dependencyCount: 0

Package: TCGAWorkflow
Version: 1.30.0
Depends: R (>= 3.4.0)
Imports: AnnotationHub, knitr, ELMER, biomaRt,
        BSgenome.Hsapiens.UCSC.hg19, circlize, c3net, ChIPseeker,
        ComplexHeatmap, ggpubr, clusterProfiler, downloader (>= 0.4),
        GenomicRanges, GenomeInfoDb, ggplot2, ggthemes, graphics,
        minet, motifStack, pathview, pbapply, parallel, rGADEM, pander,
        maftools, RTCGAToolbox, stringr, SummarizedExperiment, dplyr,
        plyr, matlab, MultiAssayExperiment, TCGAbiolinks,
        TCGAWorkflowData (>= 1.25.3), DT, gt
License: Artistic-2.0
MD5sum: 15f5ff8c5053eb8a884bfb11a93fc833
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Title: TCGA Workflow Analyze cancer genomics and epigenomics data using
        Bioconductor packages
Description: Biotechnological advances in sequencing have led to an
        explosion of publicly available data via large international
        consortia such as The Cancer Genome Atlas (TCGA), The
        Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap
        Epigenomics Mapping Consortium (Roadmap). These projects have
        provided unprecedented opportunities to interrogate the
        epigenome of cultured cancer cell lines as well as normal and
        tumor tissues with high genomic resolution. The Bioconductor
        project offers more than 1,000 open-source software and
        statistical packages to analyze high-throughput genomic data.
        However, most packages are designed for specific data types
        (e.g. expression, epigenetics, genomics) and there is no one
        comprehensive tool that provides a complete integrative
        analysis of the resources and data provided by all three public
        projects. A need to create an integration of these different
        analyses was recently proposed. In this workflow, we provide a
        series of biologically focused integrative analyses of
        different molecular data. We describe how to download, process
        and prepare TCGA data and by harnessing several key
        Bioconductor packages, we describe how to extract biologically
        meaningful genomic and epigenomic data. Using Roadmap and
        ENCODE data, we provide a work plan to identify biologically
        relevant functional epigenomic elements associated with cancer.
        To illustrate our workflow, we analyzed two types of brain
        tumors: low-grade glioma (LGG) versus high-grade glioma
        (glioblastoma multiform or GBM).
biocViews: Workflow, ResourceQueryingWorkflow
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>, Antonio Colaprico
        <antonio.colaprico@ulb.ac.be>, Catharina Olsen
        <colsen@ulb.ac.be>, Fulvio D Angelo <fulvio.dan13@gmail.com>,
        Gianluca Bontempi <gbonte@ulb.ac.be>, Michele Ceccarelli
        <m.ceccarelli@gmail.com>, Houtan Noushmehr <houtan@usp.br>
Maintainer: Tiago Chedraoui Silva <tiagochst@gmail.com>
URL: https://f1000research.com/articles/5-1542/v2
VignetteBuilder: knitr
BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues
git_url: https://git.bioconductor.org/packages/TCGAWorkflow
git_branch: RELEASE_3_20
git_last_commit: 65abf25
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/TCGAWorkflow_1.30.0.tar.gz
vignettes: vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.html
vignetteTitles: 'TCGA Workflow: Analyze cancer genomics and epigenomics
        data using Bioconductor packages'
hasREADME: FALSE
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Rfiles: vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.R
dependencyCount: 302

Package: variants
Version: 1.30.0
Depends: R (>= 3.3.0), VariantAnnotation, org.Hs.eg.db,
        TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
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Suggests: knitr, rmarkdown, BiocStyle
License: Artistic-2.0
MD5sum: f0477d9273128c7dccb02393de3ce8fd
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Title: Annotating Genomic Variants
Description: Read and write VCF files. Identify structural location of
        variants and compute amino acid coding changes for
        non-synonymous variants. Use SIFT and PolyPhen database
        packages to predict consequence of amino acid coding changes.
biocViews: ImmunoOncologyWorkflow, AnnotationWorkflow, Workflow
Author: Valerie Obenchain [aut], Martin Morgan [ctb], Bioconductor
        Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer
        <maintainer@bioconductor.org>
URL: https://bioconductor.org/help/workflows/variants/
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git_url: https://git.bioconductor.org/packages/variants
git_branch: RELEASE_3_20
git_last_commit: b0ab632
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-01
source.ver: src/contrib/variants_1.30.0.tar.gz
vignettes: vignettes/variants/inst/doc/Annotating_Genomic_Variants.html
vignetteTitles: Annotating Genomic Variants
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Rfiles: vignettes/variants/inst/doc/Annotating_Genomic_Variants.R
dependencyCount: 83