Package: CoGAPS
Version: 3.31.0
Date: 2025-03-11
Title: Coordinated Gene Activity in Pattern Sets
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
Description: 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.
Maintainer: Elana J. Fertig <ejfertig@jhmi.edu>, Thomas D. Sherman
 <tomsherman159@gmail.com>, Jeanette Johnson
 <jjohn450@jhmi.edu>, Dmitrijs Lvovs <dlvovs1@jh.edu>
Depends: R (>= 3.5.0)
Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices,
        RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats,
        SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea,
        forcats, ggplot2
Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject,
        BiocFileCache, xml2
LinkingTo: Rcpp, BH, testthat
VignetteBuilder: knitr
LazyLoad: true
License: BSD_3_clause + file LICENSE
biocViews: GeneExpression, Transcription, GeneSetEnrichment,
        DifferentialExpression, Bayesian, Clustering, TimeCourse,
        RNASeq, Microarray, MultipleComparison, DimensionReduction,
        ImmunoOncology
NeedsCompilation: yes
RoxygenNote: 7.3.2
Encoding: UTF-8
Collate: 'class-CogapsParams.R' 'CoGAPS.R' 'DistributedCogaps.R'
        'HelperFunctions.R' 'Package.R' 'RcppExports.R' 'SubsetData.R'
        'class-CogapsResult.R' 'data.R' 'methods-CogapsParams.R'
        'methods-CogapsResult.R'
Config/pak/sysreqs: make libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:05:26 UTC
RemoteUrl: https://github.com/bioc/CoGAPS
RemoteRef: HEAD
RemoteSha: 46dd3c5b05ea22877d4bba1431de2932aa46dd82
Packaged: 2026-02-08 09:27:54 UTC; root
Built: R 4.6.0; x86_64-w64-mingw32; 2026-02-08 09:31:07 UTC; windows
Archs: x64
