Package: methylGSA
Type: Package
Title: Gene Set Analysis Using the Outcome of Differential Methylation
Version: 1.28.0
Authors@R: c(
    person("Xu", "Ren", 
        email = "xuren2120@gmail.com", role = c("aut", "cre")),
    person("Pei Fen", "Kuan", 
        email = "peifen.kuan@stonybrook.edu", role = "aut"))
Description: The main functions for methylGSA are methylglm and
        methylRRA. methylGSA implements logistic regression adjusting
        number of probes as a covariate. methylRRA adjusts multiple
        p-values of each gene by Robust Rank Aggregation. For more
        detailed help information, please see the vignette.
Encoding: UTF-8
Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler,
        missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db,
        AnnotationDbi, shiny,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Depends: R (>= 3.5)
Suggests: knitr, rmarkdown, testthat, enrichplot
License: GPL-2
URL: https://github.com/reese3928/methylGSA
BugReports: https://github.com/reese3928/methylGSA/issues
RoxygenNote: 6.1.0
VignetteBuilder: knitr
biocViews:
        DNAMethylation,DifferentialMethylation,GeneSetEnrichment,Regression,
        GeneRegulation,Pathways
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:46:15 UTC
RemoteUrl: https://github.com/bioc/methylGSA
RemoteRef: RELEASE_3_22
RemoteSha: 66c5dc90c3e8c3faa1b17829363de662e1ae7897
NeedsCompilation: no
Packaged: 2026-01-24 23:35:15 UTC; root
Author: Xu Ren [aut, cre],
  Pei Fen Kuan [aut]
Maintainer: Xu Ren <xuren2120@gmail.com>
Built: R 4.5.2; ; 2026-01-24 23:52:47 UTC; windows
