R Observatory: Metrics for ssMutPA version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ssMutPA

0.1.2

Single-Sample Mutation-Based Pathway Analysis

0packages depend

2.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Junwei HanFirst published 2024-04-163 releasesCRAN page ↗

A systematic bioinformatics tool to perform single-sample mutation-based pathway analysis by integrating somatic mutation data with the Protein-Protein Interaction (PPI) network. In this method, we use local and global weighted strategies to evaluate the effects of network genes from mutations according to the network topology and then calculate the mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. Subsequently, the ssMutPES profiles are used for unsupervised spectral clustering to identify cancer subtypes.

Install

R (CRAN)Ubuntu (r2u)

install.packages("ssMutPA", 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-ssmutpa

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

13OK

Slowest check: 9.6 min · r-release-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

14

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 94%
Return-value docs: 100%
References docs: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #15,904 · ~6/day · ~174/mo

Releases R versions

Daily download trend is not available in this view yet.

20430 days

68290 days

2.1K1 year

Compare downloads with other packages →

Also on116 r2u

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (14)

ggplot2 ggridgesgrDevicesigraph kernlab maftoolsMatrixNbClustparallelpheatmap RColorBrewerstatssurvivalutils

LinkingTo (0)

none

Suggests (3)

knitr qpdf rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Junwei Han

Author, Maintainer, Copyright holder

Authors (3)

Junwei Han

Author, Maintainer, Copyright holder

Yalan He

Author

Qian Wang

Author

Copyright holders (1)

Junwei Han

Author, Maintainer, Copyright holder

Package Timeline

3 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
0.1.2Latest
2024-10-16 · current release · diff ↗
0.1.1
2024-10-10 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.0
2024-04-16
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-16
Total releases: 3 / 2 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 673 KB / 11 files
Download size: 2.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ssMutPA")

Format

Han, J., He, Y., & Wang, Q. (2024). ssMutPA: Single-Sample Mutation-Based Pathway Analysis (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.ssMutPA

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 ssMutPA version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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