CoGAPS

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see CoGAPS.

Coordinated Gene Activity in Pattern Sets

Bioconductor version: 3.18

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>, Dmitrijs Lvovs <dlvovs1 at jh.edu>

Citation (from within R, enter 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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, Clustering, DifferentialExpression, DimensionReduction, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, MultipleComparison, RNASeq, Software, TimeCourse, Transcription
Version	3.22.0
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

Suggests	testthat, knitr, rmarkdown, BiocStyle, SeuratObject
Linking To	Rcpp, BH
Enhances
Depends On Me	ATACCoGAPS
Imports Me
Suggests Me	projectR
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CoGAPS_3.22.0.tar.gz
Windows Binary	CoGAPS_3.22.0.zip
macOS Binary (x86_64)	CoGAPS_3.22.0.tgz
macOS Binary (arm64)	CoGAPS_3.22.0.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