R Observatory: Metrics for PathwayVote version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PathwayVote

0.1.3

Robust Pathway Enrichment for DNA Methylation Studies Using Ensemble Voting

0packages depend

2.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Yinan ZhengFirst published 2025-04-164 releasesCRAN page ↗

Performs pathway enrichment analysis using a voting-based framework that integrates CpG–gene regulatory information from expression quantitative trait methylation (eQTM) data. For a grid of top-ranked CpGs and filtering thresholds, gene sets are generated and refined using an entropy-based pruning strategy that balances information richness, stability, and probe bias correction. In particular, gene lists dominated by genes with disproportionately high numbers of CpG mappings are penalized to mitigate active probe bias—a common artifact in methylation data analysis. Enrichment results across parameter combinations are then aggregated using a voting scheme, prioritizing pathways that are consistently recovered under diverse settings and robust to parameter perturbations.

Install

R (CRAN)Ubuntu (r2u)

install.packages("PathwayVote", 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-pathwayvote

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: 5.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-08-05
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-23
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-07-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 17 earlier snapshots

ERROR2026-07-03
10 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE
OK2026-06-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-29
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-17
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-15
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-07
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-05
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-28
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #21,637 · ~6/day · ~178/mo

Releases R versions

Daily download trend is not available in this view yet.

15730 days

51190 days

2.1K1 year

Compare downloads with other packages →

Also on128 r2u

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (7)

harmonicmeanp AnnotationDbi clusterProfiler future furrrmethodsparallelly

LinkingTo (0)

none

Suggests (4)

GO.db org.Hs.eg.db reactome.db openxlsx

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Yinan Zheng

Author, Maintainer

Authors (1)

Yinan Zheng

Author, Maintainer

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
0.1.3Latest
2026-01-17 · current release · diff ↗
0.1.2
2025-10-01 · diff ↗
0.1.1
2025-06-25 · diff ↗
0.1.0
2025-04-16
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-16
Total releases: 4 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 15 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PathwayVote")

Format

Zheng, Y. (2026). PathwayVote: Robust Pathway Enrichment for DNA Methylation Studies Using Ensemble Voting (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.PathwayVote

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 PathwayVote 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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