title: CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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 .
authors.affiliation: Department of Oncology and Division of Oncology, Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA. ejfertig@jhmi.edu
authors.forename: Elana J
authors.initials: EJ
authors.lastname: Fertig
authors.forename: Jie
authors.initials: J
authors.lastname: Ding
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Favorov
authors.forename: Giovanni
authors.initials: G
authors.lastname: Parmigiani
authors.forename: Michael F
authors.initials: MF
authors.lastname: Ochs
mesh_terms: D019295:Computational Biology / Q000379:methods; D015870:Gene Expression; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D008390:Markov Chains; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software
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