Package: ActivePathways 2.0.5

Juri Reimand

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. Genes can be integrated using directional constraints that reflect how the input datasets are expected interact with one another. 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 recent version of the package is part of the following publication: Directional integration and pathway enrichment analysis for multi-omics data. Slobodyanyuk M^, Bahcheli AT^, Klein ZP, Bayati M, Strug LJ, Reimand J. Nature Communications (2024) <doi:10.1038/s41467-024-49986-4>.

Authors:Juri Reimand [aut, cre], Jonathan Barenboim [ctb], Mykhaylo Slobodyanyuk [aut]

ActivePathways_2.0.5.tar.gz
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ActivePathways.pdf |ActivePathways.html
ActivePathways/json (API)
NEWS

# Install 'ActivePathways' in R:
install.packages('ActivePathways', repos = c('https://reimandlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/reimandlab/activepathways/issues

On CRAN:

8.56 score 101 stars 2 packages 33 scripts 660 downloads 3 mentions 10 exports 29 dependencies

Last updated 4 months agofrom:2cd1931cfc. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:ActivePathwaysbrownsMethodDPMexport_as_CSVis.GMTmakeBackgroundmerge_p_valuesorderedHypergeometricread.GMTwrite.GMT

Dependencies:clicolorspacedata.tablefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Analysing and visualising pathway enrichment in multi-omics data using ActivePathways

Rendered fromActivePathways-vignette.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-07-28
Started: 2020-07-02