ActivePathways: Integrative Pathway Enrichment Analysis of Multivariate Omics Data

Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The package is part of the following publication: Integrative Pathway Enrichment Analysis of Multivariate Omics Data. Paczkowska M^, Barenboim J^, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group; Reimand J, PCAWG Consortium. Nature Communications (2020) <doi:10.1038/s41467-019-13983-9>.

Version: 1.0.2
Depends: R (≥ 3.6)
Imports: data.table, ggplot2
Suggests: testthat, knitr, rmarkdown, metap, EmpiricalBrownsMethod
Published: 2020-07-09
Author: Juri Reimand [aut, cre], Jonathan Barenboim [aut]
Maintainer: Juri Reimand <juri.reimand at utoronto.ca>
BugReports: https://github.com/reimandlab/ActivePathways/issues
License: GPL-3
NeedsCompilation: no
Materials: NEWS
CRAN checks: ActivePathways results

Downloads:

Reference manual: ActivePathways.pdf
Vignettes: ActivePathways
Package source: ActivePathways_1.0.2.tar.gz
Windows binaries: r-devel: ActivePathways_1.0.2.zip, r-release: ActivePathways_1.0.2.zip, r-oldrel: ActivePathways_1.0.2.zip
macOS binaries: r-release (arm64): ActivePathways_1.0.2.tgz, r-release (x86_64): ActivePathways_1.0.2.tgz, r-oldrel: ActivePathways_1.0.2.tgz
Old sources: ActivePathways archive

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