Package: recoup
Type: Package
Title: An R package for the creation of complex genomic profile plots
Author: Panagiotis Moulos <moulos@fleming.gr>
Maintainer: Panagiotis Moulos <moulos@fleming.gr>
Depends: R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2,
        ComplexHeatmap
Imports: BiocGenerics, biomaRt, Biostrings, circlize, Seqinfo,
        GenomicFeatures, graphics, grDevices, httr, IRanges, methods,
        parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats,
        stringr, txdbmaker, utils
Suggests: GenomeInfoDb, grid, BiocStyle, knitr, rmarkdown, zoo, RUnit,
        BiocManager, BSgenome, RMySQL
Description: recoup calculates and plots signal profiles created from
        short sequence reads derived from Next Generation Sequencing
        technologies. The profiles provided are either sumarized curve
        profiles or heatmap profiles. Currently, recoup supports
        genomic profile plots for reads derived from ChIP-Seq and
        RNA-Seq experiments. The package uses ggplot2 and
        ComplexHeatmap graphics facilities for curve and heatmap
        coverage profiles respectively.
License: GPL (>= 3)
Encoding: UTF-8
LazyLoad: yes
LazyData: yes
URL: https://github.com/pmoulos/recoup
biocViews: ImmunoOncology, Software, GeneExpression, Preprocessing,
        QualityControl, RNASeq, ChIPSeq, Sequencing, Coverage, ATACSeq,
        ChipOnChip, Alignment, DataImport
VignetteBuilder: knitr
Authors@R: c(person(given="Panagiotis", family="Moulos",
    email="moulos@fleming.gr", role=c("aut", "cre")))
Version: 1.39.0
Date: 2025-07-22
Collate: 'annotation.R' 'argcheck.R' 'coverage.R' 'count.R' 'plot.R'
        'profile.R' 'query.R' 'ranges.R' 'recoup.R' 'util.R'
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev perl xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:31:02 UTC
RemoteUrl: https://github.com/bioc/recoup
RemoteRef: HEAD
RemoteSha: 66d3f66b605dd24bed2748004ffd7cf6f5238e4f
NeedsCompilation: no
Packaged: 2026-01-22 20:14:22 UTC; root
Built: R 4.6.0; ; 2026-01-22 20:16:51 UTC; windows
