To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CoGAPS")
In most cases, you don't need to download the package archive at all.
CoGAPS
Coordinated Gene Activity in Pattern Sets
Bioconductor version: 2.14
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>
Citation (from within R,
enter citation("CoGAPS")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CoGAPS")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CoGAPS")
| R Script | GAPS/CoGAPS Users Manual | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, Microarray, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) |
| License | GPL (== 2) |
| Depends | R (>= 2.9.0), R.utils (>= 1.2.4), gplots (>= 2.8.0) |
| Imports | graphics, grDevices, methods, stats, utils |
| Suggests | |
| System Requirements | GAPS-JAGS (==1.0.2) |
| URL | http://sourceforge.net/p/cogapscpp/wiki/Home/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CoGAPS_1.14.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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