R Observatory: Metrics for psSubpathway version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

psSubpathway

0.1.3

Flexible Identification of Phenotype-Specific Subpathways

0packages depend

2.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Junwei HanFirst published 2019-06-214 releasesCRAN page ↗

A network-based systems biology tool for flexible identification of phenotype-specific subpathways in the cancer gene expression data with multiple categories (such as multiple subtype or developmental stages of cancer). Subtype Set Enrichment Analysis (SubSEA) and Dynamic Changed Subpathway Analysis (DCSA) are developed to flexible identify subtype specific and dynamic changed subpathways respectively. The operation modes include extraction of subpathways from biological pathways, inference of subpathway activities in the context of gene expression data, identification of subtype specific subpathways with SubSEA, identification of dynamic changed subpathways associated with the cancer developmental stage with DCSA, and visualization of the activities of resulting subpathways by using box plots and heat maps. Its capabilities render the tool could find the specific abnormal subpathways in the cancer dataset with multi-phenotype samples.

Install

R (CRAN)Ubuntu (r2u)

install.packages("psSubpathway", 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-pssubpathway

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

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 9.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

4

Dependencies · direct

Check history

NOTE2026-07-26
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-19
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-27
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 8 earlier snapshots

ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-10
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-30
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-16
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 78%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #15,054 · ~6/day · ~196/mo

Releases R versions

Daily download trend is not available in this view yet.

20130 days

69290 days

2.4K1 year

Compare downloads with other packages →

Also on421 r2u

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (4)

GSVA igraph mpmi pheatmap

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (4)

Junwei Han

no longer listed · 0.1.0 to 0.1.3

Xudong Han

no longer listed · 0.1.0 to 0.1.3

Qingfei Kong

no longer listed · 0.1.0 to 0.1.1

Qing Fei

no longer listed · 0.1.2 to 0.1.3

Package Timeline

4 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
0.1.3Latest
2024-03-18 · current release · diff ↗
0.1.2
2023-08-09 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.1
2019-10-02 · diff ↗
0.1.0
2019-06-21
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-06-21
Total releases: 4 / 7 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 3.2 MB / 9 files
Download size: 3.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("psSubpathway")

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 psSubpathway version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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