Package: sigora
Type: Package
Title: Signature Over-Representation Analysis
Version: 3.3.18
Date: 2026-08-14
Authors@R: c(
        person("Amir", "Foroushani",
        email = c("sigora.dev@gmail.com"),
        role = c("aut"),
        comment = c(ORCID = "0000-0003-2748-3009")),
        person("Fiona", "Brinkman",
        email = c("sigora.dev@gmail.com"),
        role = c("aut")),
        person("David", "Lynn",
        email = c("sigora.dev@gmail.com"),
        role = c("aut")),
        person("Witold", "Wolski",
        email = c("witold.wolski@fgcz.uzh.ch"),
        role = c("cre"),
        comment = c(ORCID = "0000-0002-6468-120X")),
        person("Travis", "Blimkie",
        email = c("travis.m.blimkie@gmail.com"),
        role = c("aut"))
        )
Depends: R (>= 3.0.0)
URL: https://github.com/wolski/sigora
BugReports: https://github.com/wolski/sigora/issues
Imports: stats, slam
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Description: Pathway analysis is a method of 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.
Encoding: UTF-8
License: GPL-3
NeedsCompilation: no
biocViews: GeneSetEnrichment, GO, Software, Pathways, KEGG
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/testthat/edition: 3
Repository: https://wolski.r-universe.dev
Date/Publication: 2026-10-30 06:58:29 UTC
RemoteUrl: https://github.com/wolski/sigora
RemoteRef: HEAD
RemoteSha: a7fd00033f128ab59114245ae65b6e862837473f
Packaged: 2026-10-30 08:53:54 UTC; root
Author: Amir Foroushani [aut] (ORCID: <https://orcid.org/0000-0003-2748-3009>),
  Fiona Brinkman [aut],
  David Lynn [aut],
  Witold Wolski [cre] (ORCID: <https://orcid.org/0000-0002-6468-120X>),
  Travis Blimkie [aut]
Maintainer: Witold Wolski <witold.wolski@fgcz.uzh.ch>