Package: pathdb 0.1.0
Aidan Frederick
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>.
Authors:
pathdb_0.1.0.tar.gz
pathdb_0.1.0.zip(r-4.7)pathdb_0.1.0.zip(r-4.6)pathdb_0.1.0.zip(r-4.5)
pathdb_0.1.0.tgz(r-4.6-any)pathdb_0.1.0.tgz(r-4.5-any)
pathdb_0.1.0.tar.gz(r-4.7-any)pathdb_0.1.0.tar.gz(r-4.6-any)
pathdb_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pathdb/json (API)
NEWS
| # Install 'pathdb' in R: |
| install.packages('pathdb', repos = c('https://aidanfred24.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/aidanfred24/pathdb/issues
Pkgdown/docs site:https://aidanfred24.github.io
- hypoxia_deseq - Hypoxia Data Differential Expression Analysis Results
- hypoxia_reads - Hypoxia Data Gene Counts
- hypoxia_T2G - Example KEGG Pathway Mapping for Hypoxia
Last updated from:09c376a4af. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 169 | ||
| source / vignettes | OK | 246 | ||
| linux-release-x86_64 | OK | 155 | ||
| macos-release-arm64 | OK | 173 | ||
| macos-oldrel-arm64 | OK | 202 | ||
| windows-devel | OK | 115 | ||
| windows-release | OK | 109 | ||
| windows-oldrel | OK | 116 | ||
| wasm-release | OK | 139 |
Exports:connect_databaseconvert_idget_genesget_pathwaysget_tablelist_tablespath_categoriespath_filterprocess_datasearch_speciesT2G_prep
Dependencies:bitbit64blobcachemclicpp11DBIdplyredgeRfastmapgenericsgluelatticelifecyclelimmalocfitmagrittrmemoisepillarpkgconfigR.methodsS3R.ooR.utilsR6rlangRSQLitestatmodtibbletidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Query Bioinformatics Database | connect_database |
| Convert Gene IDs to Ensembl | convert_id |
| Get Gene Information | get_genes |
| Get Species Pathways | get_pathways |
| Get Table from Selected Database | get_table |
| Hypoxia Data Differential Expression Analysis Results | hypoxia_deseq |
| Hypoxia Data Gene Counts | hypoxia_reads |
| Example KEGG Pathway Mapping for Hypoxia | hypoxia_T2G |
| List Table Options | list_tables |
| Retrieve Pathway Categories | path_categories |
| Filter Pathway Information By Category | path_filter |
| Process Gene Expression Data | process_data |
| Search for Species by Name | search_species |
| TERM2GENE Data Prep for iDEP Database | T2G_prep |