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Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

using rCGH package PDF R Script
Reference Manual PDF


biocViews CopyNumberVariation, FeatureExtraction, Preprocessing, Software, aCGH
Version 1.34.0
In Bioconductor since BioC 3.2 (R-3.2) (9 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,, GenomicFeatures, GenomeInfoDb, GenomicRanges, AnnotationDbi, parallel, IRanges, grDevices, aCGH
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Suggests BiocStyle, knitr, BiocGenerics, RUnit
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Follow Installation instructions to use this package in your R session.

Source Package rCGH_1.34.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) rCGH_1.34.0.tgz
macOS Binary (arm64) rCGH_1.34.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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