DOI: 10.18129/B9.bioc.CoGAPS    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CoGAPS.

Coordinated Gene Activity in Pattern Sets

Bioconductor version: 3.8

Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

Author: Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey, Genevieve Stein-O'Brien, Michael Considine, Maggie Wodicka, John Stansfield, Shawn Sivy, Carlo Colantuoni, Alexander Favorov, Mike Ochs, Elana Fertig

Maintainer: Elana J. Fertig <ejfertig at>, Thomas D. Sherman <tomsherman159 at>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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:



PDF   Reference Manual
Text   NEWS


biocViews Bayesian, Clustering, DifferentialExpression, DimensionReduction, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, MultipleComparison, RNASeq, Software, TimeCourse, Transcription
Version 3.2.40
In Bioconductor since BioC 2.7 (R-2.12) (8.5 years)
License GPL (==2)
Depends R (>= 3.5.0)
Imports BiocParallel, cluster, data.table, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5
LinkingTo Rcpp
Suggests testthat, knitr, rmarkdown, BiocStyle
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package CoGAPS_3.2.40.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) CoGAPS_3.2.40.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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: