CoGAPS

DOI: 10.18129/B9.bioc.CoGAPS    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see CoGAPS.

Coordinated Gene Activity in Pattern Sets

Bioconductor version: 3.7

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 jhmi.edu>, Thomas D. Sherman <tomsherman159 at gmail.com>

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
HTML	R Script	GWCoGAPS and PatternMarkers
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Clustering, DifferentialExpression, DimensionReduction, GeneExpression, GeneSetEnrichment, Microarray, MultipleComparison, RNASeq, Software, TimeCourse, Transcription
Version	3.0.2
In Bioconductor since	BioC 2.7 (R-2.12) (8 years)
License	GPL (==2)
Depends	R (>= 3.4.0), Rcpp (>= 0.11.0)
Imports	RColorBrewer (>= 1.0.5), gplots (>= 2.8.0), graphics, grDevices, methods, cluster, shiny, stats, utils, doParallel, foreach, ggplot2, reshape2
LinkingTo	Rcpp, BH
Suggests	testthat, lintr, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
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_3.0.2.tar.gz
Windows Binary	CoGAPS_3.0.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	CoGAPS_3.0.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CoGAPS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CoGAPS
Package Short Url	http://bioconductor.org/packages/CoGAPS/
Package Downloads Report	Download Stats