The goal of rplaza is to provide users with an R interface to the PLAZA database of plant comparative genomics. rplaza can be used to retrieve PLAZA data (e.g., genome and locus sequences, genome annotation, functional annotation, homology, etc) directly from an R session using standard R/Bioconductor data classes.
Overview
rplaza functions and the data they retrieve are summarized below:
| Function | Data retrieved | R/BioC class |
|---|---|---|
| get_genome() | Genome sequences | DNAStringSet |
| get_sequences() | Locus sequences (proteins, transcripts, CDS) | DNAStringSet / AAStringSet |
| get_annotation() | Genomic coordinates of genes | GRanges |
| get_functional_annotation() | Functional annotation (GO, InterPro, MapMan) | data.frame |
| get_tx2gene() | Transcript-to-gene ID mapping | data.frame |
| get_id_conversions() | Correspondence between alternative gene IDs | data.frame |
| get_descriptions() | Short gene descriptions | data.frame |
| get_family_assignments() | Gene family assignments | data.frame |
| get_family_functions() | Overrepresented functions for gene families | data.frame |
| get_block_duplicates() | Block (segmental or whole-genome) duplicates | data.frame |
Installation instructions
Get the latest stable R release from CRAN. Then install rplaza from Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("rplaza")And the development version from GitHub with:
BiocManager::install("almeidasilvaf/rplaza")Citation
Below is the citation output from using citation('rplaza') in R. Please run this yourself to check for any updates on how to cite rplaza.
print(citation('rplaza'), bibtex = TRUE)
#> To cite package 'rplaza' in publications use:
#>
#> Almeida-Silva F, Van de Peer Y (2025). _rplaza: R Interface to the
#> PLAZA Database for Plant Comparative Genomics_. R package version
#> 0.99.0, <https://github.com/almeidasilvaf/rplaza>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {rplaza: R Interface to the PLAZA Database for Plant Comparative Genomics},
#> author = {Fabrício Almeida-Silva and Yves {Van de Peer}},
#> year = {2025},
#> note = {R package version 0.99.0},
#> url = {https://github.com/almeidasilvaf/rplaza},
#> }If you use rplaza, please also cite:
Van Bel, M., Silvestri, F., Weitz, E. M., Kreft, L., Botzki, A., Coppens, F., & Vandepoele, K. (2022). PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants. Nucleic Acids Research, 50(D1), D1468-D1474.
Code of Conduct
Please note that the rplaza project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.