CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data

Abstract

Summary: Coordinated Gene Activity in Pattern Sets (CoGAPS) provides an integrated package for isolating gene expression driven by a biological process, enhancing inference of biological processes from transcriptomic data. CoGAPS improves on other enrichment measurement methods by combining a Markov chain Monte Carlo (MCMC) matrix factorization algorithm (GAPS) with a threshold-independent statistic inferring activity on gene sets. The software is provided as open source C++ code built on top of JAGS software with an R interface. Availability: The R package CoGAPS and the C++ package GAPS-JAGS are provided open source under the GNU Lesser Public License (GLPL) with a users manual containing installation and operating instructions. CoGAPS is available through Bioconductor and depends on the rjags package available through CRAN to interface CoGAPS with GAPS-JAGS. URL:http://www.cancerbiostats.onc.jhmi.edu/cogaps.cfm Contact:ejfertig@jhmi.edu; mfo@jhu.edu Supplementary Information: Supplementary data is available at Bioinformatics online.