recipe bioconductor-rcgh

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.







biotools: rcgh, doi: 10.1093/bioinformatics/btv718

package bioconductor-rcgh

(downloads) docker_bioconductor-rcgh


1.12.0-0, 1.10.0-0, 1.8.1-0

Depends bioconductor-acgh


Depends bioconductor-affy


Depends bioconductor-annotationdbi


Depends bioconductor-dnacopy


Depends bioconductor-genomeinfodb


Depends bioconductor-genomicfeatures


Depends bioconductor-genomicranges


Depends bioconductor-iranges


Depends bioconductor-limma




Depends bioconductor-txdb.hsapiens.ucsc.hg18.knowngene


Depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene


Depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene


Depends r-base


Depends r-ggplot2

Depends r-lattice

Depends r-mclust

Depends r-plyr

Depends r-shiny




With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-rcgh

and update with:

conda update bioconductor-rcgh

or use the docker container:

docker pull<tag>

(see bioconductor-rcgh/tags for valid values for <tag>)