recipe bioconductor-rcgh

Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data







biotools: rcgh, doi: 10.1093/bioinformatics/btv718

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.

package bioconductor-rcgh

(downloads) docker_bioconductor-rcgh



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:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-rcgh

and update with::

   mamba update bioconductor-rcgh

To create a new environment, run:

mamba create --name myenvname bioconductor-rcgh

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

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

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