tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Share:

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.

Author
January Weiner
Date of publication
2016-09-08 16:30:33
Maintainer
January Weiner <january.weiner@gmail.com>
License
GPL (>= 2.0)
Version
0.31
URLs

View on CRAN

Man pages

Egambia
Gene expression in TB patients and Healthy controls
evidencePlot
Create an evidence plot for a module
extract-methods
Shows the tmod object
getGenes
Get genes belonging to a module
getModuleMembers
Return the contents of a module
hgEnrichmentPlot
Create a visualisation of enrichment
modmetabo
Modules for metabolic profiling
pvalEffectPlot
Create an effect size / p-value plot
showGene
A combined beeswarm / boxplot
showModule
Select genes belonging to a module from a data frame
tmodAUC
Calculate AUC
tmod-class
S4 class for tmod
tmod-data
Default gene expression module data
tmodDecideTests
Count the Up- or Down-regulated genes per module
tmodImportMSigDB
Import data from MSigDB
tmodLimmaDecideTests
Up- and down-regulated genes in modules based on limma object
tmodLimmaTest
Run tmod enrichment tests directly on a limma object
tmodLimmaTopTable
tmod's replacement for the limma topTable function
tmod-package
Transcriptional Module Analysis
tmodPal
A selection of color palettes
tmodPanelPlot
Plot a summary of multiple tmod analyses
tmodPCA
PCA plot annotated with tmod
tmodSummary
Create a summary of multiple tmod analyses
tmodTagcloud
Tag cloud based on tmod results
tmodUtest
Perform a statistical test of module expression

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