TxDb.Gmax.JGI.Gmv4

TxDb.Gmax.JGI.Gmv4 provides transcript, exon, and CDS annotations for soybean (Glycine max Wm82.a4.v1). It is a Bioconductor TxDb object built from the official JGI/Phytozome GFF3 annotation; after loading you can use GenomicFeatures accessors (genes(), transcripts(), exonsBy(), cdsBy()) to extract gene models identified by JGI/Phytozome locus IDs.

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.Gmax.JGI.Gmv4)
library(AnnotationHub)
library(GenomicFeatures)

ah <- AnnotationHub()
txdb <- ah[["AH122288"]]

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

See the vignette for a full walkthrough:

vignette("vignette", package = "TxDb.Gmax.JGI.Gmv4")