Comprehensive Database for Pathway Enrichment Analysis
Overview
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.
- Initial CRAN submission.
From NEWS.md in the release
Install
Health
ERRORre-building of vignette outputsr-patched-linux-x86_64
Error(s) in re-building vignettes:
...
--- re-building ‘data-access.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘data-access.Rmd’
--- re-building ‘path-enrichment.Rmd’ using rmarkdown
Quitting from path-enrichment.Rmd:25-32 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'clusterProfiler'
---
Backtrace:
▆
1. └─base::library(clusterProfiler)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'path-enrichment.Rmd' failed with diagnostics:
there is no package called 'clusterProfiler'
--- failed re-building ‘path-enrichment.Rmd’
SUMMARY: processing the following file failed:
‘path-enrichment.Rmd’
Error: Vignette re-building failed.
Execution halted- ERROR12 OK, 1 ERROR2026-10-22
- OK13 OK2026-08-05
- NOTE12 OK, 1 NOTE2026-08-01
- OK13 OK2026-06-27
- ERROR12 OK, 1 ERROR2026-06-21
Show 3 earlier changesHide 3 earlier changes
- OK12 OK2026-06-09
- NOTE11 OK, 1 NOTE2026-06-08
- OK6 OK2026-06-04
Documentation
- Help pages
- 15 (1 internal)includes a package overview page
- Examples that run
- 100%11 run in a plain check (10 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- data-access HTML
- path-enrichment HTML
Downloads
Repository
- PRs merged (all time)
- 100%
- Median days to close, 50 most recently updated closed issues
- not measured
- Median days to close, 50 most recently updated closed PRs
- not measured
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/aidanfred24/pathdb on 2026-10-21.
GitHub Pages site last deployed 2026-06-03 · The repository has a site deploy workflow
pkgdown site last built 2026-06-03
Dependencies
Installing pathdb adds 27 packages (14 with compiled code, 12 MB of source tarballs). Heaviest: RSQLite 4.2 MB, vctrs 1.0 MB, dplyr 902 KB. 1 more not on CRAN is not measured.
Code & Tests
Datasets
People & History
- 0.1.0Latest2026-06-03 · current release
- RR 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
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("pathdb")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.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.