Package: methylGSA 1.31.0

Xu Ren

methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation

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.

Authors:Xu Ren [aut, cre], Pei Fen Kuan [aut]

methylGSA_1.31.0.tar.gz
methylGSA_1.31.0.zip(r-4.7)methylGSA_1.31.0.zip(r-4.6)methylGSA_1.31.0.zip(r-4.5)
methylGSA_1.31.0.tgz(r-4.6-any)methylGSA_1.31.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
card.svg |card.png
methylGSA/json (API)
NEWS

# Install 'methylGSA' in R:
install.packages('methylGSA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/reese3928/methylgsa/issues

Datasets:
  • cpg.pval - An example of user input cpg.pval
  • CpG2Gene - An example of user user-supplied mapping between CpGs and genes
  • GS.list - An example of user input gene sets

On BioConductor:methylGSA-1.31.0(bioc 3.24)methylGSA-1.30.0(bioc 3.23)

dnamethylationdifferentialmethylationgenesetenrichmentregressiongeneregulationpathwaysenrichmentgeneralized-linear-modelslogistic-regressionmethylationontologyshiny

7.18 score 13 stars 58 scripts 425 downloads 11 mentions 8 exports 223 dependencies

Last updated from:7792ec00a5. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE1432
linux-devel-x86_64NOTE1525
source / vignettesOK1327
linux-release-x86_64NOTE1649
macos-release-arm64NOTE839
macos-oldrel-arm64NOTE1081
windows-develNOTE1322
windows-releaseNOTE1408
windows-oldrelNOTE1230
wasm-releaseOK1160

Exports:barplotgetDescriptiongetGSmethylglmmethylgomethmethylRRAprepareAnnotrunExample

Dependencies:abindaisdkannotateAnnotationDbiapeaplotaskpassbase64base64encbeanplotBHBiasedUrnBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobbslibbumphuntercachemcallrcigarilloclicliprclusterclusterProfilercodetoolscommonmarkcpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGDOSEdplyrenrichitenrichplotevaluatefarverfastmapFDb.InfiniumMethylation.hg19filelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfsfutile.loggerfutile.optionsgdtoolsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgridExtragridGraphicsgsongtableh5mreadHDF5Arrayhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b4.hg19IlluminaHumanMethylationEPICmanifestIlluminaHumanMethylationEPICv2anno.20a1.hg38IlluminaHumanMethylationEPICv2manifestilluminaioIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimimeminfimissMethylmulttestnlmenor1mixopensslorg.Hs.eg.dbotelpatchworkpillarpkgconfigplyrpngpolyclippreprocessCoreprettyunitsprocessxprogresspromisespspurrrquadprogqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreactome.dbreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsRobustRankAggregRsamtoolsRSQLitertracklayerruvrvestS4ArraysS4VectorsS7sassscalesscatterpiescrimeselectrSeqinfoshinysiggenessnowsourcetoolsSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlyulab.utils

methylGSA: Gene Set Analysis for DNA Methylation Datasets

Xu Ren and Pei Fen Kuan

Rendered frommethylGSA-vignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-05-08
Started: 2018-06-06