CoGAPS

Coordinated Gene Activity in Pattern Sets (CoGAPS) is a software tool that identifies gene expression driven by a biological process to enhance the inference of biological processes from transcriptomic data. It combines a Markov chain Monte Carlo (MCMC) matrix factorization algorithm (GAPS) with a threshold-independent statistic that infers activity on gene sets. CoGAPS is provided as open-source C++ code built on top of JAGS software with an R interface.

Topic

Bioinformatics;Gene expression

Detail

  • Operation: Gene expression analysis

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: The 3-Clause BSD License

  • Cost: Free

  • Version name: 3.18.0

  • Credit: National Library of Medicine, National Science Foundation.

  • Input: -

  • Output: -

  • Contact: ejfertig@jhmi.edu

  • Collection: -

  • Maturity: Mature

Publications

  • CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
  • Fertig EJ, et al. CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. 2010; 26:2792-3. doi: 10.1093/bioinformatics/btq503
  • https://doi.org/10.1093/bioinformatics/btq503
  • PMID: 20810601
  • PMC: PMC3025742

Download and documentation

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