CoGAPS
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CoGAPS.
Coordinated Gene Activity in Pattern Sets
Bioconductor version: 3.17
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: Jeanette Johnson, Ashley Tsang, Jacob Mitchell, Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey, Genevieve Stein-O'Brien, Michael Considine, Maggie Wodicka, John Stansfield, Shawn Sivy, Carlo Colantuoni, Alexander Favorov, Mike Ochs, Elana Fertig
Maintainer: Elana J. Fertig <ejfertig at jhmi.edu>, Thomas D. Sherman <tomsherman159 at gmail.com>, Jeanette Johnson <jjohn450 at jhmi.edu>
citation("CoGAPS")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CoGAPS")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CoGAPS")| CoGAPS | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, Clustering, DifferentialExpression, DimensionReduction, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, MultipleComparison, RNASeq, Software, TimeCourse, Transcription |
| Version | 3.20.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (13.5 years) |
| License | BSD_3_clause + file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, biomaRt, dplyr, fgsea, forcats, ggplot2, msigdbr |
| System Requirements | |
| URL |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle |
| Linking To | Rcpp, BH |
| Enhances | |
| Depends On Me | ATACCoGAPS |
| Imports Me | projectR |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CoGAPS_3.20.0.tar.gz |
| Windows Binary | CoGAPS_3.19.0.zip |
| macOS Binary (x86_64) | CoGAPS_3.20.0.tgz |
| macOS Binary (arm64) | CoGAPS_3.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CoGAPS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CoGAPS |
| Bioc Package Browser | https://code.bioconductor.org/browse/CoGAPS/ |
| Package Short Url | https://bioconductor.org/packages/CoGAPS/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |