Package: profileplyr
Type: Package
Title: Visualization and annotation of read signal over genomic ranges
        with profileplyr
Version: 1.29.3
Date: 2025-07-22
Authors@R: c(
      person("Doug", "Barrows", email = "doug.barrows@gmail.com", role = c("aut", "cre")),
      person("Tom", "Carroll", email = "tc.infomatics@gmail.com", role = "aut"))
Depends: R (>= 3.6), BiocGenerics, SummarizedExperiment
Description: Quick and straightforward visualization of read signal
        over genomic intervals is key for generating hypotheses from
        sequencing data sets (e.g. ChIP-seq, ATAC-seq,
        bisulfite/methyl-seq). Many tools both inside and outside of R
        and Bioconductor are available to explore these types of data,
        and they typically start with a bigWig or BAM file and end with
        some representation of the signal (e.g. heatmap). profileplyr
        leverages many Bioconductor tools to allow for both flexibility
        and additional functionality in workflows that end with
        visualization of the read signal.
License: GPL (>= 3)
biocViews: ChIPSeq, DataImport, Sequencing, ChipOnChip, Coverage
Imports: GenomicRanges, stats, methods, utils, S4Vectors, R.utils,
        dplyr, magrittr, tidyr, IRanges, rjson,
        ChIPseeker,GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene,
        TxDb.Mmusculus.UCSC.mm9.knownGene,org.Hs.eg.db,org.Mm.eg.db,rGREAT,
        pheatmap, ggplot2, EnrichedHeatmap, ComplexHeatmap, grid,
        circlize, BiocParallel, rtracklayer, GenomeInfoDb, grDevices,
        rlang, tiff, Rsamtools, txdbmaker, GenomicAlignments,
        Biostrings, plyranges
Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Cairo, chipseq
VignetteBuilder: knitr
Encoding: UTF-8
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libtiff-dev libuv1-dev
        libxml2-dev libssl-dev perl xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-04 17:48:57 UTC
RemoteUrl: https://github.com/bioc/profileplyr
RemoteRef: HEAD
RemoteSha: d79bb2457a06eee1594ed2559367e07fdd3e3f14
NeedsCompilation: no
Packaged: 2026-06-04 21:41:18 UTC; root
Author: Doug Barrows [aut, cre],
  Tom Carroll [aut]
Maintainer: Doug Barrows <doug.barrows@gmail.com>