topologyGSA

1.5.0

Gene Set Analysis Exploiting Pathway Topology

0packages depend

4.5Kdownloads / year

–test coverage

10/13checks pass

Overview

About

Maintained by Gabriele SalesFirst published 2011-06-2415 releasesCRAN page ↗

Using Gaussian graphical models we propose a novel approach to perform pathway analysis using gene expression. Given the structure of a graph (a pathway) we introduce two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques). The package is based on the method described in Massa M.S., Chiogna M., Romualdi C. (2010) doi:10.1186/1752-0509-4-121.

Install

R (CRAN)Ubuntu (r2u)

install.packages("topologyGSA", repos = "https://cloud.r-project.org/")

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

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-topologygsa

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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

Health

CRAN checks

1ERROR2NOTE10OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
ERROR r-oldrel-macos-x86_64

Slowest check: 13.2 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-03-10
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 80%
References docs: 56%

Downloads

4.5K

CRAN downloads in the past year

Rank #10,989 · ~12/day · ~375/mo

Releases R versions

Daily download trend is not available in this view yet.

22730 days

91090 days

4.5K1 year

Compare downloads with other packages →

Also on115 r2u

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (6)

graph gRbase qpgraph fieldsmethodsigraph

LinkingTo (0)

none

Suggests (1)

Rgraphviz

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (2)

Sofia Massa

no longer listed · 1.0 to 1.5.0

Gabriele Sales

no longer listed · 1.0 to 1.5.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.5.0Latest
2023-09-25 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.4.7
2021-07-07 · diff ↗
unarchivedReturned to CRAN
2021-07-07
archivedRemoved from CRAN
2021-05-27
check problems were not corrected in time
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.4.6
2016-09-22 · diff ↗
R
R 3.3.0 released · 2016-05-03

Show 18 earlier events

1.4.5
2015-07-09 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.4.4
2014-08-02 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.4.3
2014-03-26 · diff ↗
1.4.2
2013-12-12 · diff ↗
1.4.1
2013-11-19 · diff ↗
1.4.0
2013-10-23 · diff ↗
1.2.1
2013-06-26 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.2.0
2013-03-01 · diff ↗
1.1.0
2012-07-18 · diff ↗
R
R 2.15.0 released · 2012-03-30
1.0.3
2011-12-22 · diff ↗
1.0.2
2011-11-10 · diff ↗
R
R 2.14.0 released · 2011-10-31
1.0
2011-06-24
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-06-24
Total releases: 15 / 15 yrs
License: GPL-3 OSI
Bundled data: 6.5 KB / 1 file
Download size: 29 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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