| Title: | AnnotationHub‑based TxDb databases for Arabidopsis, rice, and soybean |
|---|---|
| Description: | Provides TxDb (transcript database) annotations for three plant species: Arabidopsis thaliana (TAIR10), Oryza sativa (IRGSP‑1.0), and Glycine max (Wm82 v2.1), all based on Ensembl Plants release 62. The SQLite files are hosted on Zenodo and are retrieved on‑demand via AnnotationHub, keeping the package lightweight. |
| Authors: | Dwijesh Chandra Mishra [aut] (ORCID: <https://orcid.org/0000-0002-3327-6156>), Kabilan S [aut, cre] (ORCID: <https://orcid.org/0009-0002-9422-0938>), Sharanbasappa D Madival [ctb] (ORCID: <https://orcid.org/0000-0002-6571-9070>), ICAR-IARI [fnd] |
| Maintainer: | Kabilan S <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 0.99.1 |
| Built: | 2026-06-10 07:13:06 UTC |
| Source: | https://github.com/BiocStaging/PlantTxDbHub |
Provides TxDb (transcript database) annotations for three plant species: Arabidopsis thaliana (TAIR10), Oryza sativa (IRGSP‑1.0), and Glycine max (Wm82 v2.1), all based on Ensembl Plants release 62. The SQLite files are hosted on Zenodo and are retrieved on‑demand via AnnotationHub, keeping the package lightweight.
Kabilan S
Useful links:
Report bugs at https://github.com/kabilanbio/PlantTxDbHub/issues
Downloads the three plant transcript annotation databases (Arabidopsis thaliana TAIR10, Glycine max Wm82, Oryza sativa IRGSP-1.0) from Zenodo record 20606038. Files are stored in a persistent user data directory and are re-downloaded automatically if corrupted.
downloadPlantTxDbs( dest_dir = tools::R_user_dir("PlantTxDbHub", "data"), timeout = 300, download = TRUE )downloadPlantTxDbs( dest_dir = tools::R_user_dir("PlantTxDbHub", "data"), timeout = 300, download = TRUE )
dest_dir |
A character string specifying where to save the SQLite files. Defaults to a package-specific user data directory (see [tools::R_user_dir()]). |
timeout |
Numeric. Maximum download time in seconds per file. Default 300 (5 minutes). |
download |
Logical. If 'TRUE' (default), files are actually downloaded. If 'FALSE', the function only prepares the directory and returns its path without attempting any download. |
Invisibly returns the normalized path to the destination directory.
# Show the path without downloading downloadPlantTxDbs(download = FALSE) ## Not run: # Actual download (requires internet) downloadPlantTxDbs() ## End(Not run)# Show the path without downloading downloadPlantTxDbs(download = FALSE) ## Not run: # Actual download (requires internet) downloadPlantTxDbs() ## End(Not run)