To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CoGAPS")

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

CoGAPS

DOI: 10.18129/B9.bioc.CoGAPS    

This is the development version of CoGAPS; for the stable release version, see CoGAPS.

Coordinated Gene Activity in Pattern Sets

Bioconductor version: Development (3.6)

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

Maintainer: Elana J. Fertig <ejfertig at jhmi.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CoGAPS")

Documentation

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

browseVignettes("CoGAPS")

 

PDF R Script GAPS/CoGAPS Users Manual
PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, Clustering, DifferentialExpression, DimensionReduction, GeneExpression, GeneSetEnrichment, Microarray, MultipleComparison, RNASeq, Software, TimeCourse, Transcription
Version 2.11.0
In Bioconductor since BioC 2.7 (R-2.12) (7 years)
License GPL (==2)
Depends R (>= 3.0.1), Rcpp (>= 0.11.2)
Imports RColorBrewer (>= 1.0.5), gplots (>= 2.8.0), graphics, grDevices, methods, cluster, shiny, stats, utils, doParallel, foreach, ggplot2, reshape2
LinkingTo Rcpp, BH, RcppArmadillo
Suggests testthat, iterators, parallel, lintr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source CoGAPS_2.11.0.tar.gz
Windows Binary CoGAPS_2.11.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) CoGAPS_2.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CoGAPS
Package Short Url http://bioconductor.org/packages/CoGAPS/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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