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>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CoGAPS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("CoGAPS")
GAPS/CoGAPS Users Manual PDF R Script
GWCoGAPS and PatternMarkers HTML R Script
Reference Manual PDF
NEWS Text

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) (13.5 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
System Requirements
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Suggests testthat, lintr, knitr, rmarkdown, BiocStyle
Linking To Rcpp, BH
Enhances
Depends On Me
Imports Me
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Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/CoGAPS/
Package Short Url https://bioconductor.org/packages/CoGAPS/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive