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.


Version 0.36, 09.03.2018:

  • corrected notorious problems with CRAN
  • please CRAN have mercy
  • I will sacrifice a virtual goat before submitting
  • changed parameter "order.by" to "sort.by" in tmodLimmaTest
  • added function pcaplot; tmod no longer depends on pca3d due to notorious problems with installing rgl on students Mac computers
  • limma examples now wrapped in if(require(limma))...

Version 0.34, 10.08.2017:

  • added filter.rows.auc option

Version 0.32:

  • Added tmodZtest and tmodWZtest
  • Modified gene.labels option for evidencePlot

Version 0.31:

  • Use of the plotwidgets package for pvalEffectPlot (rug, boxpie and pie options)

Version 0.30:

  • Apparently, knitr cache got packed in the package itself, blowing up its size ten fold.

Version 0.29:

  • A last minute bugfix

Version 0.28:

  • Added simpleBoxpie - rectangular plots that are thought better to visualize areas than regular pie charts
  • added a few palette functions from my personal repertoire

Version 0.27:

  • Introduced metabolic modules and created a vignette section for a case study in metabolomic
  • changed the return object of tmodPCA()
  • added the "extra" parameter to showModule(); showModule() can take a data frame or a vector now
  • added "row.labels.style" parameter to tmodPanelPlot()

Version 0.25:

  • corrected the malfunctioning testthat test. I HATE TESTTHAT. (Also, I read it as "test t hat" - and wonder about estimates and Student's t)

Version 0.24:

  • msigDB is broken, it no longer has unique identifiers in the global XML file. I corrected the import function to make sure identifiers are unique.
  • pvalEffectPlot was expecting log10(p-values) rather than p-values. This has been taken care of.
  • evidencePlot can now generate GSEA-style curves (with the "style" option)

Version 0.22:

  • added Cohen's d estimate and t statistic to tmodLimmaTopTable()
  • rewrote evidencePlot: it is now much more flexible

Reference manual

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0.40 by January Weiner, 3 months ago


Browse source code at https://github.com/cran/tmod

Authors: January Weiner

Documentation:   PDF Manual  

GPL (>= 2.0) license

Imports beeswarm, tagcloud, XML, methods, plotwidgets

Suggests testthat, knitr, rmarkdown, pca3d, limma

Imported by disco.

See at CRAN