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: 1.40.0 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: Bioconductor 3.23 Date/Publication: 2026-04-28 12:43:06 UTC RemoteUrl: https://github.com/bioc/recoup RemoteRef: RELEASE_3_23 RemoteSha: 4a9a71fb53ae54e197b9970299c5e66bde05f623 NeedsCompilation: no Packaged: 2026-10-01 12:03:12 UTC; root