Package 'TxDb.Gmax.JGI.Gmv4'

Title: Transcripts Annotation Database for Soybean
Description: 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 and is available via AnnotationHub (retrievable with AnnotationHub()); after loading you can use GenomicFeatures accessors (genes(), transcripts(), exonsBy(), cdsBy()) to extract gene models identified by JGI/Phytozome locus IDs.
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>), ICAR-IARI [fnd]
Maintainer: Kabilan S <[email protected]>
License: Artistic-2.0
Version: 0.99.1
Built: 2026-10-04 11:34:43 UTC
Source: https://github.com/BiocStaging/TxDb.Gmax.JGI.Gmv4

Help Index

Annotation package for TxDb object(s)

Description

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 and is available via AnnotationHub (retrievable with AnnotationHub()); after loading you can use GenomicFeatures accessors (genes(), transcripts(), exonsBy(), cdsBy()) to extract gene models identified by JGI/Phytozome locus IDs.

Note

This data package was built from the JGI/Phytozome GFF3 annotation of soybean (Glycine max Wm82.a4.v1).

Author(s)

Dwijesh Chandra Mishra (aut), Sharanbasappa D Madival (aut), Kabilan S (aut, cre) [email protected]

See Also

transcripts, transcriptsBy

Examples

## The TxDb object is downloaded from AnnotationHub, so this example is
## only run when AnnotationHub is installed and the resource is
## reachable.
if (requireNamespace("AnnotationHub", quietly=TRUE)) {
    txdb <- tryCatch({
        ah <- AnnotationHub::AnnotationHub()
        ah[["AH122288"]]
    }, error=function(e) NULL)

    if (!is.null(txdb)) {
        txdb
        ## retrieve all genes
        GenomicFeatures::genes(txdb)
    }
}