CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data
Fertig, Elana J.
Favorov, Alexander V.
Ochs, Michael F.
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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.
Fertig, E., Favorov, A., Ochs, M., Ding, J., & Parmigiani, G. (2010). CoGAPS: An R/C++ package to identify patterns and biological process activity in transcriptomic data. Bioinformatics, 26(21), 2792-2793.
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