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pathdb  

Comprehensive Database for Pathway Enrichment Analysis
View on CRAN: Click here


Download and install pathdb package within the R console
Install from CRAN:
install.packages("pathdb")

Install from Github:
library("remotes")
install_github("cran/pathdb")

Install by package version:
library("remotes")
install_version("pathdb", "0.1.0")



Attach the package and use:
library("pathdb")
Maintained by
Aidan Frederick
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-06-03
Latest Update: 2026-06-03
Description:
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>.
How to cite:
Aidan Frederick (2026). pathdb: Comprehensive Database for Pathway Enrichment Analysis. R package version 0.1.0, https://cran.r-project.org/web/packages/pathdb. Accessed 25 Oct. 2026.
Previous versions and publish date:
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Complete documentation for pathdb
Functions, R codes and Examples using the pathdb R package
Full pathdb package functions and examples
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