PathNet: An R package for pathway analysis using topological information

PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.

Author
Bhaskar Dutta <bhaskar.dutta@gmail.com>, Anders Wallqvist <awallqvist@bhsai.org>, and Jaques Reifman <jreifman@bhsai.org>
Date of publication
None
Maintainer
Jason B. Smith <jsmith@bhsai.org>
License
GPL-3
Version
1.14.0

View on Bioconductor

Man pages

PathNet
Enrichment and contextual analysis of KEGG pathways

Files in this package

PathNet/DESCRIPTION
PathNet/NAMESPACE
PathNet/R
PathNet/R/PathNet.R
PathNet/R/context_functions.R
PathNet/R/enrichment_functions.R
PathNet/build
PathNet/build/vignette.rds
PathNet/inst
PathNet/inst/CITATION
PathNet/inst/doc
PathNet/inst/doc/PathNet.R
PathNet/inst/doc/PathNet.Rnw
PathNet/inst/doc/PathNet.pdf
PathNet/inst/unitTests
PathNet/inst/unitTests/test_contextual.R
PathNet/inst/unitTests/test_enrichment.R
PathNet/inst/unitTests/test_setup.R
PathNet/man
PathNet/man/PathNet.Rd
PathNet/tests
PathNet/tests/runTests.R
PathNet/vignettes
PathNet/vignettes/Contextual_association_between_pathways.txt
PathNet/vignettes/Direct_indirect_combined_evidence.txt
PathNet/vignettes/PathNet.Rnw
PathNet/vignettes/PathNet_IO.png
PathNet/vignettes/PathNet_enrichment_results.txt
PathNet/vignettes/Pathway_overlap.txt