To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CoGAPS")
In most cases, you don't need to download the package archive at all.
CoGAPS
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Coordinated Gene Activity in Pattern Sets
Bioconductor version: Release (3.5)
Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.
Author: Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey, Genevieve Stein-O'Brien, Michael Considine, John Stansfield, Shawn Sivy, Carlo Colantuoni, Alexander Favorov, Mike Ochs, Elana Fertig
Maintainer: Elana J. Fertig <ejfertig at jhmi.edu>
Citation (from within R,
enter citation("CoGAPS")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://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 | Bayesian, Clustering, DifferentialExpression, DimensionReduction, GeneExpression, GeneSetEnrichment, Microarray, MultipleComparison, RNASeq, Software, TimeCourse, Transcription |
| Version | 2.10.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (7 years) |
| License | GPL (==2) |
| Depends | R (>= 3.0.1), Rcpp (>= 0.11.2) |
| Imports | RColorBrewer (>= 1.0.5), gplots (>= 2.8.0), graphics, grDevices, methods, cluster, shiny, stats, utils, doParallel, foreach, ggplot2, reshape2 |
| LinkingTo | Rcpp, BH, RcppArmadillo |
| Suggests | testthat, iterators, parallel, lintr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CoGAPS_2.10.0.tar.gz |
| Windows Binary | CoGAPS_2.10.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | CoGAPS_2.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CoGAPS |
| Package Short Url | http://bioconductor.org/packages/CoGAPS/ |
| Package Downloads Report | Download Stats |
Documentation »
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