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/

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Files in this package

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.

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