This repository is a fork of cran/sigora repository https://github.com/cran/sigora
Package ‘sigora’ was removed from the CRAN repository. It was archived on 2021-04-10 as check problems were not corrected in time.
The code changes made in the project aim at removing all ERROR’s and
WARNING’s from the R CMD check and
BiocCheck.
Pathway Analysis is statistically linking observations on the
molecular level to biological processes or pathways on the systems(i.e.,
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.
However, this can lead to identifying spurious 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 datasets. In addition, it contains pre-computed
Pathway-GPS data for pathways in the KEGG and Reactome pathway
repositories and mechanisms for extracting GPS for user-supplied
repositories.
Author: Amir B.K. Foroushani
remoteds::install_githug("wolski/sigora")For more information about the Sigora package, see: wolski.github.io/sigora