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ActivePathways
View on CRAN: Click
here
Download and install ActivePathways package within the R console
Install from CRAN:
install.packages("ActivePathways")
Install from Github:
library("remotes")
install_github("cran/ActivePathways")
Install by package version:
library("remotes")
install_version("ActivePathways", "2.0.3")
Attach the package and use:
library("ActivePathways")
Maintained by
Juri Reimand
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-05-04
Latest Update: 2023-08-11
Description:
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 first version of 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) .
How to cite:
Juri Reimand (2019). ActivePathways: Integrative Pathway Enrichment Analysis of Multivariate Omics Data. R package version 2.0.3, https://cran.r-project.org/web/packages/ActivePathways
Previous versions and publish date:
Other packages that cited ActivePathways R package
View ActivePathways citation profile
Other R packages that ActivePathways depends,
imports, suggests or enhances
Functions, R codes and Examples using
the ActivePathways R package
Some associated functions: ActivePathways . DPM . GMT . brownsMethod . columnSignificance . enrichmentAnalysis . export_as_CSV . hypergeometric . makeBackground . merge_p_values . orderedHypergeometric . prepareCytoscape .
Some associated R codes: Full ActivePathways package functions and examples
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