To install this package, start R and enter:

## try http:// if https:// URLs are not supported

In most cases, you don't need to download the package archive at all.



This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see rCGH.

Comprehensive Pipeline for Analyzing and Visualizing Agilent and Affymetrix Array-Based CGH Data

Bioconductor version: 3.2

A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through Agilent and Affymetrix microarrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, and Affymetrix SNP6.0 and cytoScan probeset.txt, cychp.txt, and cnchp.txt files, exported from ChAS or Affymetrix Power Tools. This package takes over all the steps required for a genomic profile analysis, from reading the files to the segmentation and genes annotations, and provides several visualization functions (static or interactive) which facilitate profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.

Author: Frederic Commo [aut, cre]

Maintainer: Frederic Commo <frederic.commo at>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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



PDF using rCGH package
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, FeatureExtraction, Preprocessing, Software, aCGH
Version 1.0.2
In Bioconductor since BioC 3.2 (R-3.2) (0.5 years)
License Artistic-2.0
Depends R (>= 3.2.1), methods
Imports plyr, DNAcopy, lattice, aCGH, ggplot2, grid, shiny (>= 0.11.1), limma, affy, mclust, TxDb.Hsapiens.UCSC.hg19.knownGene,, GenomicFeatures, GenomeInfoDb, GenomicRanges, AnnotationDbi, parallel, stats, utils, graphics, IRanges, grDevices
Suggests BiocStyle, knitr, BiocGenerics, RUnit
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source rCGH_1.0.2.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) rCGH_1.0.2.tgz
Mac OS X 10.9 (Mavericks) rCGH_1.0.2.tgz
Subversion source (username/password: readonly)
Git source
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center