sigora

3.2.0

Signature Overrepresentation Analysis

0packages depend

4.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Witold WolskiFirst published 2012-06-146 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("sigora")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

pak::pak("wolski/sigora")

Development version from wolski/sigora. Requires the pak package.

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-sigora

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

bspm (used by r2u) also needs make: sudo apt install make

sudo dnf copr enable iucar/cran

sudo dnf install R-CRAN-sigora

RPMs from the iucar/cran COPR, rebuilt from CRAN.

sudo zypper install R-sigora

RPMs auto-built from CRAN on openSUSE OBS.

Health

CRAN checks

13OK

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-29
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

4.8K

CRAN downloads in the past year

Rank #9,527 · ~13/day · ~397/mo

37230 days

1.2K90 days

4.8K1 year

Also on132 r2u22 autocran237 conda_forge38 c2d4u

Source & community

GitHub ↗

Repository stars, issues, and contributor activity are not tracked yet.

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (2)

stats baseslam

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code

1,734Lines of code

7Exported functions

Code & tests

Open call graph →

Code intelligence has not been computed for this package yet.

People & History

People (4)

Maintainer (1)

Witold Wolski iD

Maintainer

Authors (3)

Fiona Brinkman

Author

Amir Foroushani iD

Author

David Lynn

Author

Release timeline

6 releases. Pick two to compare their code metrics; R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
3.2.0Latest
2026-03-21 · current release
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
3.1.1
2021-11-30 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
3.0.5
2019-08-23 · diff ↗
R
R 3.6.0 released · 2019-04-26
3.0.1
2018-09-28 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
2.0.1
2016-05-11 · diff ↗
R
R 3.3.0 released · 2016-05-03

Show 4 earlier events

R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
0.9.2
2012-06-14

Package metadata

First published: 2012-06-14
Total releases: 6 / 14 yrs
License: GPL-3 OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet