Package: rCGH
Type: Package
Title: Comprehensive Pipeline for Analyzing and Visualizing Array-Based
        CGH Data
Version: 1.39.1
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: 2025-07-26 01:36:40 UTC; biocbuild
Author: Frederic Commo [aut, cre]
git_url: https://git.bioconductor.org/packages/rCGH
git_branch: devel
git_last_commit: e2612d3
git_last_commit_date: 2025-07-24
Repository: Bioconductor 3.22
Date/Publication: 2025-07-25
Built: R 4.5.1; ; 2025-07-26 13:53:20 UTC; windows
