Package: GenomicPlot
Type: Package
Title: Plot profiles of next generation sequencing data in genomic
        features
Version: 1.8.1
Authors@R: person("Shuye", "Pu", email = "shuye2009@gmail.com", role = c("aut", "cre"), 
   comment = c(ORCID = "0000-0002-6664-8438"))
Description: Visualization of next generation sequencing (NGS) data is
        essential for interpreting high-throughput genomics experiment
        results. 'GenomicPlot' facilitates plotting of NGS data in
        various formats (bam, bed, wig and bigwig); both coverage and
        enrichment over input can be computed and displayed with
        respect to genomic features (such as UTR, CDS, enhancer), and
        user defined genomic loci or regions. Statistical tests on
        signal intensity within user defined regions of interest can be
        performed and represented as boxplots or bar graphs. Parallel
        processing is used to speed up computation on multicore
        platforms. In addition to genomic plots which is suitable for
        displaying of coverage of genomic DNA (such as ChIPseq data),
        metagenomic (without introns) plots can also be made for RNAseq
        or CLIPseq data as well.
License: GPL-2
Encoding: UTF-8
LazyData: FALSE
Collate: "DrawingFunctions.R" "GenomicPlot.R" "HandleDataMatrix.R"
        "HandleFeatures.R" "Parallel.R" "ReadData.R" "Setup.R"
        "Plot_5parts_metagene.R" "Plot_start_end.R"
        "Plot_start_end_with_random.R" "Plot_region.R" "Plot_locus.R"
        "data.R" "Plot_locus_with_random.R" "Plot_peak_annotation.R"
        "Plot_bam_correlation.R"
Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1)
Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0),
        plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram,
        ggplotify, Seqinfo, IRanges, ComplexHeatmap, RCAS (>= 1.20.0),
        scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR,
        circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), ggpubr,
        grDevices, graphics, stats, utils, GenomicFeatures, genomation
        (>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics,
        dplyr, grid
Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat,
        AnnotationDbi, GenomeInfoDb
biocViews: AlternativeSplicing, ChIPSeq, Coverage, GeneExpression,
        RNASeq, Sequencing, Software, Transcription, Visualization,
        Annotation
RoxygenNote: 7.3.2
VignetteBuilder: knitr
BugReports: https://github.com/shuye2009/GenomicPlot/issues
URL: https://github.com/shuye2009/GenomicPlot
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev perl libx11-dev xz-utils
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-12-08 21:21:58 UTC
RemoteUrl: https://github.com/bioc/GenomicPlot
RemoteRef: RELEASE_3_22
RemoteSha: 5f4c44d78a9954ce44b2fbdb7e43b059a61c68c5
NeedsCompilation: no
Packaged: 2025-12-09 04:11:14 UTC; root
Author: Shuye Pu [aut, cre] (ORCID: <https://orcid.org/0000-0002-6664-8438>)
Maintainer: Shuye Pu <shuye2009@gmail.com>
Built: R 4.5.2; ; 2025-12-09 04:14:45 UTC; windows
