sigora: Signature Overrepresentation Analysis

Pathway Analysis is the process of statistically linking observations on the molecular level to biological processes or pathways on the systems (organism, organ, tissue, cell) level. Traditionally, pathway analysis methods regard pathways as collections of single genes and treat all genes in a pathway as equally informative. This can lead to identification of spurious (misleading) pathways as statistically significant, since components are often shared amongst pathways. SIGORA seeks to avoid this pitfall by focusing on genes or gene-pairs that are (as a combination) specific to a single pathway. In relying on such pathway gene-pair signatures (Pathway-GPS), SIGORA inherently uses the status of other genes in the experimental context to identify the most relevant pathways. The current version allows for pathway analysis of human and mouse data sets and contains pre-computed Pathway-GPS data for pathways in the KEGG and Reactome pathway repositories as well as mechanisms for extracting GPS for user supplied repositories.

Version: 2.0.1
Depends: R (≥ 2.10)
Imports: utils, stats
Suggests: slam
Published: 2016-05-11
Author: Amir B.K. Foroushani, Fiona S.L. Brinkman, David J. Lynn
Maintainer: Amir Foroushani <sigora.dev at gmail.com>
License: GPL-2
NeedsCompilation: no
Citation: sigora citation info
CRAN checks: sigora results

Downloads:

Reference manual: sigora.pdf
Package source: sigora_2.0.1.tar.gz
Windows binaries: r-devel: sigora_2.0.1.zip, r-release: sigora_2.0.1.zip, r-oldrel: sigora_2.0.1.zip
OS X El Capitan binaries: r-release: sigora_2.0.1.tgz
OS X Mavericks binaries: r-oldrel: sigora_2.0.1.tgz
Old sources: sigora archive

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