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)

# Install 'tmod' in R:
install.packages('tmod', repos = c('https://january3.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Datasets:
  • Egambia - Gene expression in TB patients and Healthy controls
  • EgambiaResults - Gene expression in TB patients and Healthy controls
  • cell_signatures - Cell type signatures
  • modmetabo - Modules for metabolic profiling
  • tbmprof - Modules for metabolic profiling
  • tmod - Default gene expression module data
  • vaccination - Transcriptomic responses to vaccination

On CRAN:

6.87 score 3 stars 1 packages 164 scripts 392 downloads 18 mentions 51 exports 48 dependencies

Last updated 2 years agofrom:1c5f882e78. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-winNOTEOct 26 2024
R-4.5-linuxNOTEOct 26 2024
R-4.4-winNOTEOct 26 2024
R-4.4-macNOTEOct 26 2024
R-4.3-winNOTEOct 26 2024
R-4.3-macNOTEOct 26 2024

Exports:as_tmodGScheck_tmod_gseigengeneevidencePlotfilterGSgetGenesgetModuleMembersggEvidencePlotggPanelplothgEnrichmentPlotmakeTmodmakeTmodFromDataFramemakeTmodGSmodCorPlotmodcorsmodGroupsmodjaccardmodOverlapspcaplotpvalEffectPlotshowGeneshowModulesimpleBoxpiesimplePiesimpleRugtmod_idstmod_ids<-tmod_titlestmod_titles<-tmod2DataFrametmod2tmodGStmodAUCtmodCERNOtesttmodDecideTeststmodGeneSetTesttmodHGtesttmodImportMSigDBtmodLEAtmodLEASummarytmodLimmaDecideTeststmodLimmaTesttmodLimmaTopTabletmodPaltmodPanelPlottmodPCAtmodPLAGEtesttmodSummarytmodTagcloudtmodUtesttmodZtestupset

Dependencies:beeswarmbitopscaToolsclicolorspacecpp11dplyrfansifarvergenericsggplot2ggrepelgluegplotsgtablegtoolsisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepheatmappillarpkgconfigplotwidgetspurrrR6RColorBrewerRcpprlangscalesstringistringrtagcloudtibbletidyrtidyselectutf8vctrsviridisLitewithrXML

tmod: Analysis of Gene Set Enrichments

January Weiner

Rendered fromtmod.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2022-09-26
Started: 2022-02-10

Readme and manuals

Help Manual

Help pageTopics
Transcriptional Module Analysistmod-package
Cell type signaturescell_signatures
Check an object of class tmodGScheck_tmod_gs
Gene expression in TB patients and Healthy controlsEgambia EgambiaResults
Calculate the eigengene of a module from a data seteigengene
Create an evidence plot for a moduleevidencePlot
Filter by genes belonging to a gene set from a data framefilterGS showModule
Get genes belonging to a gene setgetGenes
Return the contents of a gene setgetModuleMembers
Create an evidence plot for a module (ggplot2 version)ggEvidencePlot
Create a tmod panel plot using ggplotggPanelplot
Create a visualisation of enrichmenthgEnrichmentPlot
Convert a data frame to a tmod objectmakeTmodFromDataFrame
S3 class for tmod gene set collectionsas_tmodGS length.tmodGS makeTmod makeTmodGS print.tmodGS [.tmod [.tmodGS
Plot a correlation heatmap for modulesmodCorPlot
Module correlationmodcors
Find group of modulesmodGroups
Jaccard index for modulesmodjaccard
Modules for metabolic profilingmodmetabo tbmprof
Calculate overlaps of the modulesmodOverlaps
Plot a PCA object returned by prcomppcaplot
Create an effect size / p-value plotpvalEffectPlot
A combined beeswarm / boxplotshowGene
Simple Pie ChartsimpleBoxpie simplePie simpleRug
Query and set IDs of gene sets in a tmodGS objecttmod_ids tmod_ids<- tmod_titles tmod_titles<-
Default gene expression module datatmod tmod-data
Convert a tmod module set into a data frametmod2DataFrame
Convert the old tmod objects to the tmodGS objectstmod2tmodGS
Calculate AUCtmodAUC
Count the Up- or Down-regulated genes per moduletmodDecideTests
Import data from MSigDBtmodImportMSigDB
Leading Edge AnalysistmodLEA
Summary stats of a leading edge analysistmodLEASummary
Up- and down-regulated genes in modules based on limma objecttmodLimmaDecideTests
Run tmod enrichment tests directly on a limma objecttmodLimmaTest
tmod's replacement for the limma topTable functiontmodLimmaTopTable
A selection of color palettestmodPal
Plot a summary of multiple tmod analysestmodPanelPlot
PCA plot annotated with tmodtmodPCA
Create a summary of multiple tmod analysestmodSummary
Tag cloud based on tmod resultstmodTagcloud
Perform a statistical test of module expressiontmodCERNOtest tmodGeneSetTest tmodHGtest tmodPLAGEtest tmodUtest tmodZtest
Upset plotupset
Transcriptomic responses to vaccinationvaccination