Package: rCGH
Type: Package
Title: Comprehensive Pipeline for Analyzing and Visualizing Array-Based
        CGH Data
Version: 1.43.0
Date: 2025-07-24
Authors@R: c(person(given="Frederic", family="Commo", role=c("aut", "cre"), 
    email="fredcommo@gmail.com"))
Maintainer: Frederic Commo <fredcommo@gmail.com>
URL: https://github.com/fredcommo/rCGH
Description: A comprehensive pipeline for analyzing and interactively
        visualizing genomic profiles generated through commercial or
        custom aCGH arrays. As inputs, rCGH supports Agilent dual-color
        Feature Extraction files (.txt), from 44 to 400K, Affymetrix
        SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt
        files exported from ChAS or Affymetrix Power Tools. rCGH also
        supports custom arrays, provided data complies with the
        expected format. This package takes over all the steps required
        for individual genomic profiles analysis, from reading files to
        profiles segmentation and gene annotations. This package also
        provides several visualization functions (static or
        interactive) which facilitate individual profiles
        interpretation. Input files can be in compressed format, e.g.
        .bz2 or .gz.
License: Artistic-2.0
biocViews: aCGH,CopyNumberVariation,Preprocessing,FeatureExtraction
Depends: R (>= 3.4),methods,stats,utils,graphics
Imports: plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1),
        limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene,
        TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,
        org.Hs.eg.db,GenomicFeatures,Seqinfo,GenomicRanges,AnnotationDbi,
        parallel,IRanges,grDevices,aCGH
Suggests: BiocStyle, knitr, BiocGenerics, RUnit
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2026-05-19 10:25:09 UTC; root
Author: Frederic Commo [aut, cre]
Config/pak/sysreqs: cmake make libbz2-dev liblzma-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:41:31 UTC
RemoteUrl: https://github.com/bioc/rCGH
RemoteRef: HEAD
RemoteSha: 834c831ded5c35bc8e4ca951e2e4a1c6df48a9fe
Built: R 4.6.0; ; 2026-05-19 10:34:26 UTC; unix
