LEANR: Finds "Local Subnetworks" Within an Interaction Network which Show Enrichment for Differentially Expressed Genes

Implements the method described in "Network-based analysis of omics data: The LEAN method" [Gwinner Boulday (2016) <doi:10.1093/bioinformatics/btw676>] Given a protein interaction network and a list of p-values describing a measure of interest (as e.g. differential gene expression) this method computes an enrichment p-value for the protein neighborhood of each gene and compares it to a background distribution of randomly drawn p-values. The resulting scores are corrected for multiple testing and significant hits are returned in tabular format.

Version: 1.4.9
Depends: R (≥ 2.14), igraph (≥ 0.7.1), foreach (≥ 1.4.2)
Suggests: knitr, doMC, rmarkdown, ROCR, testthat
Published: 2016-11-12
Author: Frederik Gwinner
Maintainer: Frederik Gwinner <frederik.gwinner at gmail.com>
License: GPL-3
NeedsCompilation: no
Materials: README
CRAN checks: LEANR results

Downloads:

Reference manual: LEANR.pdf
Vignettes: LEAN on CCM data
LEAN on simulated subnetworks
Package source: LEANR_1.4.9.tar.gz
Windows binaries: r-devel: LEANR_1.4.9.zip, r-release: LEANR_1.4.9.zip, r-oldrel: LEANR_1.4.9.zip
OS X Mavericks binaries: r-release: LEANR_1.4.9.tgz, r-oldrel: LEANR_1.4.9.tgz

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