Package: ActivePathways 2.0.5
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:
ActivePathways_2.0.5.tar.gz
ActivePathways_2.0.5.zip(r-4.5)ActivePathways_2.0.5.zip(r-4.4)ActivePathways_2.0.5.zip(r-4.3)
ActivePathways_2.0.5.tgz(r-4.4-any)ActivePathways_2.0.5.tgz(r-4.3-any)
ActivePathways_2.0.5.tar.gz(r-4.5-noble)ActivePathways_2.0.5.tar.gz(r-4.4-noble)
ActivePathways_2.0.5.tgz(r-4.4-emscripten)ActivePathways_2.0.5.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/reimandlab/activepathways/issues
Last updated 3 months agofrom:2cd1931cfc. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 13 2024 |
R-4.5-win | OK | Oct 13 2024 |
R-4.5-linux | OK | Oct 13 2024 |
R-4.4-win | OK | Oct 13 2024 |
R-4.4-mac | OK | Oct 13 2024 |
R-4.3-win | OK | Oct 13 2024 |
R-4.3-mac | OK | Oct 13 2024 |
Exports:ActivePathwaysbrownsMethodDPMexport_as_CSVis.GMTmakeBackgroundmerge_p_valuesorderedHypergeometricread.GMTwrite.GMT
Dependencies:clicolorspacedata.tablefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
ActivePathways | ActivePathways |
Merge p-values using the Brown's method. | brownsMethod |
Determine which terms are found to be significant using each column individually. | columnSignificance |
Merge p-values using the DPM method. | DPM |
Export the results from ActivePathways as a comma-separated values (CSV) file. | export_as_CSV |
Read and Write GMT files | GMT gmt is.GMT read.GMT write.GMT |
Hypergeometric test | hypergeometric |
Make a background list of genes (i.e., the statistical universe) based on all the terms (gene sets, pathways) considered. | makeBackground |
Merge a list or matrix of p-values | merge_p_values |
Ordered Hypergeometric Test | orderedHypergeometric |
Prepare files for building an enrichment map network visualization in Cytoscape | prepareCytoscape |