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.

AuthorJanuary Weiner
Date of publication2016-09-08 16:30:33
MaintainerJanuary Weiner <january.weiner@gmail.com>
LicenseGPL (>= 2.0)
Version0.31
http://bioinfo.mpiib-berlin.mpg.de/tmod/

View on CRAN

Functions

[ Man page
Egambia Man page
evidencePlot Man page
getGenes Man page
getModuleMembers Man page
hgEnrichmentPlot Man page
makeTmod Man page
modmetabo Man page
pvalEffectPlot Man page
show Man page
showGene Man page
showModule Man page
show,tmod-method Man page
tbmprof Man page
tmod Man page
tmodAUC Man page
tmodCERNOtest Man page
tmod-class Man page
tmod-data Man page
tmodDecideTests Man page
tmodHGtest Man page
tmodImportMSigDB Man page
tmodLimmaDecideTests Man page
tmodLimmaTest Man page
tmodLimmaTopTable Man page
[,tmod-method Man page
tmod-package Man page
tmodPal Man page
tmodPanelPlot Man page
tmodPCA Man page
tmodSummary Man page
tmodTagcloud Man page
tmodUtest Man page

Files

tmod
tmod/inst
tmod/inst/doc
tmod/inst/doc/tmod.R
tmod/inst/doc/tmod.pdf
tmod/inst/doc/tmod.rmd
tmod/tests
tmod/tests/testthat.R
tmod/tests/testthat
tmod/tests/testthat/sample_data.csv
tmod/tests/testthat/res_HG.csv
tmod/tests/testthat/test_tests.R
tmod/tests/testthat/res_CERNO.csv
tmod/tests/testthat/test_data.R
tmod/tests/testthat/res_U.csv
tmod/NAMESPACE
tmod/NEWS
tmod/data
tmod/data/Egambia.rda
tmod/data/tbmprof.rda
tmod/data/modmetabo.rda
tmod/data/datalist
tmod/data/tmod.rda
tmod/R
tmod/R/modmetabo.R tmod/R/classes.R tmod/R/multivariate.R tmod/R/helpers.R tmod/R/importexport.R tmod/R/tmod-data.R tmod/R/visualizations.R tmod/R/Egambia.R tmod/R/statisticaltests.R tmod/R/limma.R tmod/R/panelplots.R tmod/R/tmod-package.R
tmod/vignettes
tmod/vignettes/bibliography.bib
tmod/vignettes/tmod.rmd
tmod/MD5
tmod/build
tmod/build/vignette.rds
tmod/DESCRIPTION
tmod/man
tmod/man/getGenes.Rd tmod/man/modmetabo.Rd tmod/man/tmodAUC.Rd tmod/man/tmodPCA.Rd tmod/man/hgEnrichmentPlot.Rd tmod/man/tmodImportMSigDB.Rd tmod/man/getModuleMembers.Rd tmod/man/tmodSummary.Rd tmod/man/Egambia.Rd tmod/man/tmodPanelPlot.Rd tmod/man/tmodLimmaTopTable.Rd tmod/man/pvalEffectPlot.Rd tmod/man/tmodPal.Rd tmod/man/showGene.Rd tmod/man/tmodLimmaDecideTests.Rd tmod/man/evidencePlot.Rd tmod/man/extract-methods.Rd tmod/man/tmod-class.Rd tmod/man/tmodUtest.Rd tmod/man/tmodTagcloud.Rd tmod/man/tmod-package.Rd tmod/man/tmodLimmaTest.Rd tmod/man/showModule.Rd tmod/man/tmod-data.Rd tmod/man/tmodDecideTests.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.