pathdb
Comprehensive Database for Pathway Enrichment Analysis
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>.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 27, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 21, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: ... --- re-building ‘data-access.Rmd’ using rmarkdown --- finished re-building ‘data-access.Rmd’ --- re-building ‘path-enrichment.Rmd’ using rmarkdown Quitting from path-enrichment.Rmd:25-32 [setup] ~~~~~~~~~~~~ ...[truncated]... ment.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
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
NOTE 11 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 8, 2026
CRAN incoming feasibility
Maintainer: ‘Aidan Frederick <Aidan.Frederick@sdstate.edu>’ Reading Rd files failed with message: cannot open the connection