Package: tmod 0.50.13

tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Methods and feature set definitions for feature or gene set enrichment analysis in transcriptional and metabolic profiling data. Package includes tests for enrichment based on ranked lists of features, functions for visualisation and multivariate functional analysis. See Zyla et al (2019) <doi:10.1093/bioinformatics/btz447>.

Authors:January Weiner [aut, cre]

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tmod.pdf |tmod.html✨
tmod/json (API)

Peer review:

Bug tracker:https://github.com/january3/tmod/issues

On CRAN:

51 exports 3 stars 3.32 score 48 dependencies 1 dependents 18 mentions 140 scripts 410 downloads

Last updated 1 years agofrom:1c5f882e78. Checks:OK: 1 NOTE: 6. Indexed: yes.

Exports:as_tmodGScheck_tmod_gseigengeneevidencePlotfilterGSgetGenesgetModuleMembersggEvidencePlotggPanelplothgEnrichmentPlotmakeTmodmakeTmodFromDataFramemakeTmodGSmodCorPlotmodcorsmodGroupsmodjaccardmodOverlapspcaplotpvalEffectPlotshowGeneshowModulesimpleBoxpiesimplePiesimpleRugtmod_idstmod_ids<-tmod_titlestmod_titles<-tmod2DataFrametmod2tmodGStmodAUCtmodCERNOtesttmodDecideTeststmodGeneSetTesttmodHGtesttmodImportMSigDBtmodLEAtmodLEASummarytmodLimmaDecideTeststmodLimmaTesttmodLimmaTopTabletmodPaltmodPanelPlottmodPCAtmodPLAGEtesttmodSummarytmodTagcloudtmodUtesttmodZtestupset

Dependencies:beeswarmbitopscaToolsclicolorspacecpp11dplyrfansifarvergenericsggplot2ggrepelgluegplotsgtablegtoolsisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepheatmappillarpkgconfigplotwidgetspurrrR6RColorBrewerRcpprlangscalesstringistringrtagcloudtibbletidyrtidyselectutf8vctrsviridisLitewithrXML