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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PathNet")
AuthorBhaskar Dutta <bhaskar.dutta@gmail.com>, Anders Wallqvist <awallqvist@bhsai.org>, and Jaques Reifman <jreifman@bhsai.org>
Bioconductor views DifferentialExpression KEGG MultipleComparison Network NetworkEnrichment Pathways
Date of publicationNone
MaintainerJason B. Smith <jsmith@bhsai.org>
LicenseGPL-3
Version1.16.0

View on Bioconductor

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.