pathdb: Comprehensive Database for Pathway Enrichment Analysis

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>.

Version:	0.1.0
Depends:	R (≥ 4.1.0)
Imports:	DBI, dplyr, edgeR, R.utils, RSQLite, stats, utils, tools
Suggests:	clusterProfiler, curl, knitr, rmarkdown, testthat (≥ 3.0.0)
Published:	2026-06-03
DOI:	10.32614/CRAN.package.pathdb (may not be active yet)
Author:	Aidan Frederick [aut, cre], Xijin Ge [fnd]
Maintainer:	Aidan Frederick <Aidan.Frederick at sdstate.edu>
BugReports:	https://github.com/aidanfred24/pathdb/issues
License:	GPL (≥ 3)
URL:	https://github.com/aidanfred24/pathdb, https://aidanfred24.github.io/pathdb/
NeedsCompilation:	no
Language:	en-US
Materials:	README, NEWS
CRAN checks:	pathdb results

Documentation:

Reference manual:	pathdb.html , pathdb.pdf
Vignettes:	data-access (source, R code) path-enrichment (source, R code)

Downloads:

Package source:	pathdb_0.1.0.tar.gz
Windows binaries:	r-devel: not available, r-release: pathdb_0.1.0.zip, r-oldrel: not available
macOS binaries:	r-release (arm64): pathdb_0.1.0.tgz, r-oldrel (arm64): pathdb_0.1.0.tgz, r-release (x86_64): pathdb_0.1.0.tgz, r-oldrel (x86_64): pathdb_0.1.0.tgz

Linking:

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