Package: pathdb
Type: Package
Title: Comprehensive Database for Pathway Enrichment Analysis
Version: 0.1.0
Authors@R: c(
    person(
      "Aidan", "Frederick",
      email = "Aidan.Frederick@sdstate.edu",
      role = c("aut", "cre")
    ),
    person(
      "Xijin", "Ge",
      email = "Xijin.Ge@sdstate.edu",
      role = c("fnd")
    )
  )
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>. 
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Language: en-US
Imports: DBI, dplyr, edgeR, R.utils, RSQLite, stats, utils, tools
RoxygenNote: 7.3.3
Suggests: clusterProfiler, curl, knitr, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Depends: R (>= 4.1.0)
URL: https://github.com/aidanfred24/pathdb,
        https://aidanfred24.github.io/pathdb/
BugReports: https://github.com/aidanfred24/pathdb/issues
Config/Needs/editorial: spelling
NeedsCompilation: no
Packaged: 2026-05-29 23:02:25 UTC; aidan
Author: Aidan Frederick [aut, cre],
  Xijin Ge [fnd]
Maintainer: Aidan Frederick <Aidan.Frederick@sdstate.edu>
Repository: CRAN
Date/Publication: 2026-06-03 13:00:02 UTC
Built: R 4.5.3; ; 2026-08-24 04:18:01 UTC; windows
