Multivariate Pathway Enrichment Analysis

An integrative method of analyzing multi omics data that conducts enrichment analysis of annotated gene sets. 'ActivePathways' uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes, improving systems-level understanding of cellular organization in health and disease.


activePathways 1.0.1

Major Changes

  • Rename to activePathways

activeDriverPW 1.0.0

Major Changes

  • Add a geneset.filter option to activeDriverPW to filter the GMT by geneset size
  • Add vignettes
  • Export merge_p_values method


Major changes

  • Rename to activeDriverPW


Major Changes

  • Change column contribution method. Column contribution is now reported as the log-fold-change when the column is excluded. ie, -log10(p_val_with_column / p_val_without_column)

Minor Changes

  • No longer raises an error if no significant terms are found and return.all is false. Instead returns an empty data.table and issues a warning.
  • Issue a warning if genes are filtered out for not being found in the background
  • Change default p-value adjustment method to "holm"
  • If return.all==FALSE, calculates columnContribution only for terms that will returned. Speeds up runtime by roughly a factor of 2
  • Add "none" option to p-value adjustment methods
  • New implementation of orderedHypergeometric function which is several times faster.

Bug fixes

  • Fix Brown's method when all p-values in a column are the same
  • Fix in orderedHypergeometric which added an extra NA to the complement, leading to small errors in the calculated p-value
  • Fixed another bug in orderedHypergeometric which added an extra NA to the complement in some cases, leading to small errors in the calculated p-value


  • Initial Build

  • Added a file to track changes to the package.

Reference manual

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1.0.1 by Helen Zhu, a year ago

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Browse source code at

Authors: Helen Zhu [aut, cre] , Juri Reimand [aut] , Jonathan Barenboim [aut]

Documentation:   PDF Manual  

GPL-3 license

Imports metap, data.table, ggplot2

Suggests testthat, knitr, rmarkdown

See at CRAN