Name Mode Size
..
CoGAPS.Rmd 100755 16 kb
CoGAPS.html 100755 812 kb
References.bib 100755 2 kb
README.md
# CoGAPS Version: 3.2.40 [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS) [![downloads](https://bioconductor.org/shields/downloads/release/CoGAPS.svg)](http://bioconductor.org/packages/stats/bioc/CoGAPS/) [![Build Status](https://travis-ci.org/FertigLab/CoGAPS.svg?branch=master)](https://travis-ci.org/FertigLab/CoGAPS) 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. # Installing CoGAPS *CoGAPS* is a bioconductor R package and so the release version can be installed as follows: ``` install.packages("BiocManager") BiocManager::install("CoGAPS") ``` The most up-to-date version of *CoGAPS* can be installed directly from the *FertigLab* Github Repository: ``` ## Method 1 using BiocManager BiocManager::install("FertigLab/CoGAPS") ## Method 2 using devtools package devtools::install_github("FertigLab/CoGAPS") ``` # Using CoGAPS Follow the vignette here: http://htmlpreview.github.io/?https://github.com/FertigLab/CoGAPS/blob/develop/vignettes/CoGAPS.html