R Observatory: Metrics for ssMutPA version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ssMutPA

0.1.2Package record

Single-Sample Mutation-Based Pathway Analysis

0packages depend

2.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Junwei HanCRAN 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. 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

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-08
ERROR12 OK, 1 ERROR2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.2

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 23
Examples that run: 100%11 run in a plain check
Exported functions with examples: 92%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

ssMutPA HTML

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #15,046 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

29530 days

80490 days

2.4K1 year

Compare downloads with other packages →

Also on72 r2u

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing ssMutPA adds 24 packages (10 with compiled code, 22 MB of source tarballs). Heaviest: ggplot2 6.0 MB, igraph 4.8 MB, ggridges 2.1 MB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Junwei Han

Yalan He

Author

Qian Wang

Author

Releases (3)

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
0.1.2Latest
record
2024-10-16 · current release · diff ↗
0.1.1
record
2024-10-10 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.0
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →