About the project

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-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures

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

HowTO install the Sigora package

remoteds::install_githug("wolski/sigora")

For more information about the Sigora package, see: wolski.github.io/sigora

CRAN submission

1. Ensure a clean check with no errors, warnings, or notes:

make check

2. Run CRAN-specific incoming checks:

devtools::check(remote = TRUE, manual = TRUE)

3. Submit to CRAN via devtools::release() (interactive, recommended):

devtools::release()

Or manually:

# Build the tarball
R CMD build .

# Upload sigora_3.1.1.tar.gz at:
# 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.