Installation | Install from Bioconductor | Install the development version from GitHub | Introduction | Finding available species | Downloading the databases | Loading a TxDb (Arabidopsis example) | Available columns and keys | Retrieve all genes | Retrieve all transcripts | Retrieve all exons | Filter by gene ID | Retrieving transcript types | Working with chromosome names | Soybean (Glycine max) example | Rice (Oryza sativa) example | Contributing new species | Data sources and licensing | Session information
Package: PlantTxDbHub 0.99.6
Kabilan S
PlantTxDbHub: Transcript Database Hub for Plant Genomes
Provides TxDb (transcript database) annotations for plant species. The SQLite files are hosted on Zenodo (or other permanent URLs) and are downloaded on demand via the `downloadPlantTxDbs()` function. The list of available species and their download URLs is maintained in a curated CSV file (inst/extdata/metadata.csv), allowing users and contributors to easily add new databases without modifying R code.
Authors:
PlantTxDbHub_0.99.6.tar.gz
PlantTxDbHub_0.99.6.zip(r-4.7-any)PlantTxDbHub_0.99.6.zip(r-4.6-any)PlantTxDbHub_0.99.6.zip(r-4.5-any)
PlantTxDbHub_0.99.6.tgz(r-4.6-any)PlantTxDbHub_0.99.6.tgz(r-4.5-any)
PlantTxDbHub_0.99.6.tar.gz(r-4.7-any)PlantTxDbHub_0.99.6.tar.gz(r-4.6-any)
PlantTxDbHub_0.99.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PlantTxDbHub/json (API)
| # Install 'PlantTxDbHub' in R: |
| install.packages('PlantTxDbHub', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kabilanbio/planttxdbhub/issues
annotationdatatxdbarabidopsis_thalianaoryza_sativaglycine_maxsequenceannotation
Last updated from:b38f8940d9. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 171 | ||
| linux-devel | OK | 207 | ||
| source / vignettes | OK | 318 | ||
| linux-release | OK | 187 | ||
| macos-release | OK | 131 | ||
| macos-oldrel | OK | 142 | ||
| windows-devel | OK | 115 | ||
| windows-release | OK | 150 | ||
| windows-oldrel | OK | 145 | ||
| wasm-release | OK | 143 |
Exports:downloadPlantTxDbsgetTxDbPathgetTxDbProvenancelistPlantTxDbSpecies
Dependencies:askpassBiocFileCachebitbit64blobcachemclicpp11curlDBIdbplyrdplyrfastmapfilelockgenericsgluehttr2lifecyclemagrittrmemoiseopensslpillarpkgconfigpurrrR6rlangRSQLitestringistringrsystibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| PlantTxDbHub: TxDb databases for plants | PlantTxDbHub-package PlantTxDbHub |
| Download plant TxDb SQLite files from Zenodo (or other sources) | downloadPlantTxDbs |
| Get the local path to a cached TxDb SQLite file | getTxDbPath |
| Show data provider and source information for a species | getTxDbProvenance |
| List available plant TxDb species | listPlantTxDbSpecies |
