Package: methylGSA 1.23.0
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:
methylGSA_1.23.0.tar.gz
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methylGSA.pdf |methylGSA.html✨
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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
On BioConductor:methylGSA-1.23.0(bioc 3.20)methylGSA-1.22.0(bioc 3.19)
Last updated 2 months agofrom:54e1b7fb99
Exports:barplotgetDescriptiongetGSmethylglmmethylgomethmethylRRAprepareAnnotrunExample
Dependencies:abindannotateAnnotationDbiapeaplotaskpassbase64base64encbeanplotBHBiasedUrnBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibbumphuntercachemclicliprclusterProfilercodetoolscolorspacecommonmarkcowplotcpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoRNGDOSEdownloaderdplyrenrichplotfansifarverfastmapfastmatchFDb.InfiniumMethylation.hg19fgseafontawesomeforeachformatRfsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeglueGO.dbGOSemSimgraphlayoutsgridExtragridGraphicsgsongtableHDF5ArrayHDO.dbhmshtmltoolshttpuvhttrigraphIlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b4.hg19IlluminaHumanMethylationEPICmanifestIlluminaHumanMethylationEPICv2anno.20a1.hg38IlluminaHumanMethylationEPICv2manifestilluminaioIRangesisobanditeratorsjquerylibjsonliteKEGGRESTlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimissMethylmulttestmunsellnlmenor1mixopensslorg.Hs.eg.dbpatchworkpillarpkgconfigplogrplyrpngpolyclippreprocessCoreprettyunitsprogresspromisespurrrquadprogqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreactome.dbreadrreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRobustRankAggregRsamtoolsRSQLitertracklayerruvS4ArraysS4VectorssassscalesscatterpiescrimeshadowtextshinysiggenessnowsourcetoolsSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttidytreetreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrXMLxml2xtableXVectoryamlyulab.utilszlibbioc