TxDb.Athaliana.Ensembl.TAIR10

TxDb.Athaliana.Ensembl.TAIR10 provides transcript, exon, CDS, and gene annotations for Arabidopsis thaliana based on the TAIR10 reference genome. It is a Bioconductor TxDb object built from the Ensembl Plants GFF3 annotation (Ensembl Plants release 63), covering the TAIR10 nuclear chromosomes and organellar genomes.

After loading the package, you can use GenomicFeatures accessors such as genes(), transcripts(), exonsBy(), and cdsBy() to extract and query gene models from the TAIR10 annotation.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install(c("AnnotationHub", "GenomicFeatures"))

Usage

The TxDb object is not shipped inside the package; it is hosted on AnnotationHub and downloaded on first use.

library(TxDb.Athaliana.Ensembl.TAIR10)
library(AnnotationHub)
library(GenomicFeatures)

ah <- AnnotationHub()
txdb <- ah[["AH122287"]]

genes(txdb)
head(transcripts(txdb))
exonsBy(txdb, by = "tx")

See the vignette for a full walkthrough:

vignette("vignette", package = "TxDb.Athaliana.Ensembl.TAIR10")