DOI: 10.18129/B9.bioc.rCGH    

Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

Bioconductor version: Release (3.14)

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.

Author: Frederic Commo [aut, cre]

Maintainer: Frederic Commo <fredcommo at gmail.com>

Citation (from within R, enter citation("rCGH")):


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PDF R Script using rCGH package
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, FeatureExtraction, Preprocessing, Software, aCGH
Version 1.24.0
In Bioconductor since BioC 3.2 (R-3.2) (6 years)
License Artistic-2.0
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, GenomeInfoDb, GenomicRanges, AnnotationDbi, parallel, IRanges, grDevices, aCGH
Suggests BiocStyle, knitr, BiocGenerics, RUnit
URL https://github.com/fredcommo/rCGH
Depends On Me
Imports Me preciseTAD
Suggests Me excluderanges
Links To Me
Build Report  

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Follow Installation instructions to use this package in your R session.

Source Package rCGH_1.24.0.tar.gz
Windows Binary rCGH_1.24.0.zip
macOS 10.13 (High Sierra) rCGH_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rCGH
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rCGH
Package Short Url https://bioconductor.org/packages/rCGH/
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Old Source Packages for BioC 3.14 Source Archive

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