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sigora  

Signature Overrepresentation Analysis
View on CRAN: Click here


Download and install sigora package within the R console
Install from CRAN:
install.packages("sigora")

Install from Github:
library("remotes")
install_github("cran/sigora")

Install by package version:
library("remotes")
install_version("sigora", "3.1.1")



Attach the package and use:
library("sigora")
Maintained by
Witold Wolski
[Scholar Profile | Author Map]
First Published: 2012-06-14
Latest Update: 2021-11-30
Description:
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 andReactome pathway repositories and mechanisms for extracting GPS for user-supplied repositories.
How to cite:
Witold Wolski (2012). sigora: Signature Overrepresentation Analysis. R package version 3.1.1, https://cran.r-project.org/web/packages/sigora. Accessed 29 Mar. 2025.
Previous versions and publish date:
0.9.2 (2012-06-14 16:33), 2.0.1 (2016-05-11 00:26), 3.0.1 (2018-09-28 20:30), 3.0.5 (2019-08-23 20:20)
Other packages that cited sigora R package
View sigora citation profile
Other R packages that sigora depends, imports, suggests or enhances
Complete documentation for sigora
Functions, R codes and Examples using the sigora R package
Some associated functions: genesFromRandomPathways . getGenes . getURL . idmap . kegH . kegM . load_data . makeGPS . nciTable . ora . reaH . reaM . sigora-package . sigora . 
Some associated R codes: aa_package.R . genesFromRandomPathways.R . getGenes.R . getURL.R . load_data.R . makeGPS.R . ora.R . sigora-package.R . sigora.R .  Full sigora package functions and examples
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