CoGAPS requires GAPS-JAGS available from http://sourceforge.net/p/cogapscpp/wiki/Home/, http://www.rits.onc.jhmi.edu/dbb/custom/A6/CoGAPS.cfm, or http://astor.som.jhmi.edu/~ejfertig/ejfertig/Software.html.  This c++ package is a redistribution of JAGS version 2.1.0 with a module implementing the GAPS matrix decomposition for microarray data.  Please see the installation instructions in the users manual.  If you have any questions, please comment Elana Fertig <ejfertig@jhmi.edu> or Michael Ochs <mfo@jhu.edu>.

01Sep2011 - Removed dependency on rjags package on CRAN
02Sep2011 - Included loading of jags libraries upon package loading to avoid setting the LD_LIBRARY_PATH variable
01Aug2012 - Incorporated statistic to quantify inferred membership of each gene in a specified gene set with corresponding examples published in Fertig, Favorov, and Ochs (2012) IEEE Conference on Bioinformatics and Biomedicine (B310). 
02Jan2013 - Updated link to software
03Mar2013 - Added smooth plotting and utilities to do pattern matching and updated statistic from August to work with multiple contexts
15Jul2013 - Added processed data from Colantuoni et al. (2011) Temporal dynamics and genetic control of transcription in the human prefrontal cortex. Nature, 478:519-523 used for Fertig et al. (2013) Pattern identification in time course gene expression data with the CoGAPS matrix factorization. Chapter 6 in MF Ochs (ed) Methods in Molecular Biology: Gene Function Analysis, 2nd Edition, Springer, New York.
