R Observatory: Metrics for pathdb version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pathdb

0.1.0

Comprehensive Database for Pathway Enrichment Analysis

0packages depend

844downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Aidan FrederickFirst published 2026-06-031 releasesCRAN page ↗GitHub ↗

Provides access to large-scale genomics data from the South Dakota State University's bioinformatics database, a unified platform for pathway analysis of over 13,000 organisms. It includes various gene mappings, gene characteristics, and pathway mapping data from KEGG, GOBP, GOCC, and many more pathway databases. Also provides various helper functions for processing RNA-Seq data for differential expression analysis and pathway enrichment analysis, occasionally sourced from code from Integrated Differential Expression & Pathway analysis (iDEP), developed by Ge, S.X., Son, E.W. & Yao, R. (2018) doi:10.1186/s12859-018-2486-6.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("pathdb", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("aidanfred24/pathdb")

Development version from aidanfred24/pathdb. Installs pak first if it is not already available.

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-pathdb

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: 2.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.26

not tracked

Coverage

100%

Documentation · exports

8

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

NOTE2026-06-08
11 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-04
6 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 251 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

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

Downloads

844

CRAN downloads in the past year

Rank #11,634 · ~2/day · ~70/mo

Releases R versions

Daily download trend is not available in this view yet.

22730 days

84490 days

8441 year

Compare downloads with other packages →

Also on17 r2u

Repository

GitHub ↗ aidanfred24/pathdb

0Stars

0Forks

2Open issues

0Open PRs

0Releases

License GPL-3.0 · Last activity 2026-06-27

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/aidanfred24/pathdb on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (8)

DBI dplyr edgeR R.utils RSQLitestatsutilstools

LinkingTo (0)

none

Suggests (5)

clusterProfiler curl knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Aidan Frederick

Author, Maintainer

Authors (1)

Aidan Frederick

Author, Maintainer

Funders (1)

Xijin Ge

Funder

Package Timeline

1 release. R releases are shown for context.

0.1.0Latest
2026-06-03 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-03
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 868 KB / 3 files
Download size: 4.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pathdb")

Format

Frederick, A., & Ge, X. (2026). pathdb: Comprehensive Database for Pathway Enrichment Analysis (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.pathdb

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 pathdb version 0.1.0 [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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