Package: sigora
Type: Package
Title: Signature Overrepresentation Analysis
Version: 3.2.0
Date: 2026-03-21
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"))
        )
Depends: R (>= 3.0.0)
URL: https://github.com/wolski/sigora
BugReports: https://github.com/wolski/sigora/issues
Imports: stats, slam
Suggests: knitr, rmarkdown
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 and Reactome pathway repositories and mechanisms for
        extracting GPS for user-supplied repositories.
Encoding: UTF-8
License: GPL-3
NeedsCompilation: no
biocViews: GeneSetEnrichment, GO, Software, Pathways, KEGG
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Repository: https://wolski.r-universe.dev
Date/Publication: 2026-03-21 18:41:40 UTC
RemoteUrl: https://github.com/wolski/sigora
RemoteRef: HEAD
RemoteSha: 7a1e905c415a4e9173554b482d1f1ecf64235285
Packaged: 2026-06-19 08:02:03 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>)
Maintainer: Witold Wolski <witold.wolski@fgcz.uzh.ch>