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-Amplitude.pdf 100644 5 kb
-Patterns.pdf 100644 5 kb
AppNote.bib 100644 43 kb
CoGAPSUsersManual-concordance.tex 100644 0 kb
CoGAPSUsersManual.Rnw 100644 23 kb
CoGAPSUsersManual.bbl 100644 2 kb
CoGAPSUsersManual.log 100644 29 kb
CoGAPSUsersManual.synctex.gz 100644 101 kb
CoGAPSUsersManual.tex 100644 34 kb
CoGAPSUsersManual.toc 100644 2 kb
GISTFigs-Amplitude.pdf 100644 45 kb
GISTFigs-Patterns.pdf 100644 5 kb
GWCoGAPSPMs.pdf 100644 174 kb
GWCoGAPSvignette.Rmd 100644 6 kb
GWCoGAPSvignette.html 100644 816 kb
ManPipePMs.pdf 100644 13 kb
ShinyApp.pdf 100644 317 kb
ShinyApp.png 100644 61 kb
ShinyApp.tiff 100644 124 kb
chicago.sty 100644 10 kb
example_matched_ps.RData 100644 1 kb
example_partition_1.RData 100644 5 kb
example_partition_2.RData 100644 5 kb
README.md
# CoGAPS [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS) [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS) [![Travis-CI Build Status](https://travis-ci.org/CoGAPS/CoGAPS.svg?branch=master)](https://travis-ci.org/CoGAPS/CoGAPS) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/CoGAPS/CoGAPS?branch=master&svg=true)](https://ci.appveyor.com/project/CoGAPS/CoGAPS) [![Coverage Status](https://img.shields.io/codecov/c/github/CoGAPS/CoGAPS/master.svg)](https://codecov.io/github/CoGAPS/CoGAPS?branch=master) 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.