Identifying relevant pathways based on the over-representation of gene-pair signatures
Pathway analysis is a method to 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 from user-supplied repositories.
Amir B.K. Foroushani
This repository is a fork of cran/sigora repository https://github.com/cran/sigora
Package SIGORA was removed from the CRAN repository and archived on 2021-04-10 as check problems were not corrected in time. It has since been updated and is now available from CRAN once more.
The code changes made in the project aim at removing all errors and
warnings from R CMD check and BiocCheck.
From CRAN:
install.packages("sigora")
From Github:
# remotes::install_github("wolski/sigora")
install.packages("sigora", repos = c('https://wolski.r-universe.dev', 'https://cloud.r-project.org'))
For more information about the Sigora package, see: wolski.github.io/sigora
make check
devtools::check(remote = TRUE, manual = TRUE)
devtools::release() (interactive, recommended):devtools::release()
Or manually build the tarball with R CMD build . and upload it to: https://cran.r-project.org/submit.html.
The manual form asks for the tarball, your name, email (must match the maintainer in DESCRIPTION), and an optional comment to CRAN reviewers. You will receive a confirmation email; the submission is not complete until you click the link in that email.