R Observatory: Metrics for topologyGSA version 1.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

topologyGSA

1.5.0Package record

Gene Set Analysis Exploiting Pathway Topology

0packages depend

4.7Kdownloads / year

–test coverage

10/13flavors OK

Overview

About

Maintained by Gabriele SalesCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

1ERROR2NOTE10OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-x86_64

Package required but not available: ‘qpgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Gabriele Sales <gabriele.sales@unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sofia",
                      family = "Massa",
                      role = "aut"),
               person(given = "Gabriele",
                      family = "Sales",
                      role = c("aut", "cre"),
                      email = "gabriele.sales@unipd.it"))
as necessary.

CRAN check page ↗

Slowest check: 9.0 min · r-oldrel-windows-x86_64

Status changes

ERROR10 OK, 2 NOTE, 1 ERRORNow
ERROR11 OK, 2 NOTE, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.5.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9
Examples that run: 100%5 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 80%
Help pages citing references: 56%

How these are measured

Downloads

4.7K

CRAN downloads in the past year

Rank #9,712 · ~13/day · ~390/mo

Releases R versions

Daily download trend is not available in this view yet.

40130 days

1K90 days

4.7K1 year

Compare downloads with other packages →

Also on86 r2u

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing topologyGSA adds 19 packages (14 with compiled code, 25 MB of source tarballs). Heaviest: igraph 4.8 MB, fields 3.9 MB, spam 3.1 MB. 2 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (2)

Sofia Massa

Gabriele Sales

Maintainer since 1.2.0 (2012), previously Sofia Massa (1.0 to 1.1.0)

Releases (15)

Pick two releases to compare their code metrics.

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
record
2023-09-25 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-07-07
1.4.7
record
2021-07-07 · diff ↗
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
record
2016-09-22 · diff ↗
R
R 3.3.0 released · 2016-05-03

Show 18 earlier eventsHide 18 earlier events

1.4.5
record
2015-07-09 · diff ↗ ·
removed 4 exports
print.clique.var.test, print.clique.mean.test, print.pathway.var.test, print.pathway.mean.test
R
R 3.2.0 released · 2015-04-16
1.4.4
record
2014-08-02 · diff ↗ ·
added 4 exports
print.clique.var.test, print.clique.mean.test, print.pathway.var.test, print.pathway.mean.test
R
R 3.1.0 released · 2014-04-10
1.4.3
record
2014-03-26 · diff ↗
1.4.2
record
2013-12-12 · diff ↗
1.4.1
record
2013-11-19 · diff ↗
1.4.0
record
2013-10-23 · diff ↗
1.2.1
record
2013-06-26 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.2.0
record
2013-03-01 · diff ↗
1.1.0
record
2012-07-18 · diff ↗
R
R 2.15.0 released · 2012-03-30
1.0.3
record
2011-12-22 · diff ↗
1.0.2
record
2011-11-10 · diff ↗
R
R 2.14.0 released · 2011-10-31
1.0
record
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 · relicensed from AGPL-3 in 1.4.4
Bundled data: 6.5 KB / 1 file
Download size: 29 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("topologyGSA")

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for topologyGSA version 1.5.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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