CoGAPS

Coordinated Gene Activity in Pattern Sets

Bioconductor version: 2.8

Coordinated Gene Activity in Pattern Sets (CoGAPS) infers biological processes which are active in individual gene sets from corresponding microarray measurements. CoGAPS achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets.

Author: Elana J. Fertig

Maintainer: Elana J. Fertig <ejfertig at jhmi.edu>, Michael F. Ochs <mfo at jhu.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("CoGAPS")

To cite this package in a publication, start R and enter:

    citation("CoGAPS")

Documentation

PDF R Script GAPS/CoGAPS Users Manual
PDF   Reference Manual

Details

biocViews GeneExpression, Microarray, Bioinformatics
Depends R (>= 2.9.0), rjags(>= 2.1.0), R.utils (>= 1.2.4)
Imports graphics, grDevices, methods, stats, utils
Suggests
System Requirements GAPS-JAGS (==1.0.2)
License GPL (== 2)
URL http://www.cancerbiostats.onc.jhmi.edu/cogaps.cfm
Depends On Me
Imports Me
Suggests Me
Version 1.2.0
Since Bioconductor 2.7 (R-2.12)

Package Downloads

Package Source CoGAPS_1.2.0.tar.gz
Windows Binary
MacOS 10.5 (Leopard) binary
Package Downloads Report Download Stats

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Fred Hutchinson Cancer Research Center