Pathway enrichment analysis enables researchers to uncover mechanisms underlying the phenotype. pathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies active subnetworks in a protein-protein interaction network using user-provided a list of genes. It performs pathway enrichment analyses on the identified subnetworks. pathfindR also offers functionalities to cluster enriched pathways and identify representative pathways and to score the pathways per sample. The method is described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv. <doi:10.1101/272450>.
| Version: | 1.2.1 |
| Depends: | R (≥ 3.4), knitr, shiny |
| Imports: | AnnotationDbi, DBI, doParallel, foreach, rmarkdown, org.Hs.eg.db, ggplot2, fpc, pathview |
| Published: | 2018-08-17 |
| Author: | Ege Ulgen, Ozan Ozisik |
| Maintainer: | Ege Ulgen <egeulgen at gmail.com> |
| BugReports: | https://github.com/egeulgen/pathfindR/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/egeulgen/pathfindR |
| NeedsCompilation: | no |
| SystemRequirements: | Java JVM 1.8 |
| Citation: | pathfindR citation info |
| Materials: | NEWS |
| CRAN checks: | pathfindR results |
| Reference manual: | pathfindR.pdf |
| Vignettes: |
pathfindR - An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks |
| Package source: | pathfindR_1.2.1.tar.gz |
| Windows binaries: | r-devel: pathfindR_1.2.1.zip, r-release: pathfindR_1.2.1.zip, r-oldrel: pathfindR_1.2.1.zip |
| OS X binaries: | r-release: not available, r-oldrel: not available |
| Old sources: | pathfindR archive |
Please use the canonical form https://CRAN.R-project.org/package=pathfindR to link to this page.