Package: recoup Type: Package Title: An R package for the creation of complex genomic profile plots Author: Panagiotis Moulos Maintainer: Panagiotis Moulos 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: 1.41.0 Date: 2026-03-23 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: 2026-04-28 12:43:06 UTC RemoteUrl: https://github.com/bioc/recoup RemoteRef: HEAD RemoteSha: ad7ae07e1e1e5fc1894a97c4674d8943788be8c1 NeedsCompilation: no Packaged: 2026-06-18 11:23:35 UTC; root