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TxDb.Osativa.MSU.RGAP7

This is the development version of TxDb.Osativa.MSU.RGAP7; to use it, please install the devel version of Bioconductor.

Transcript Annotation Database for Rice


Bioconductor version: Development (3.24)

Provides transcript, exon, and CDS annotations for Oryza sativa (rice) as a Bioconductor TxDb object, generated from the Rice Genome Annotation Project (RGAP) Release 7 / MSU7 GFF3 file (genome assembly IRGSP-1.0). The TxDb object is distributed through AnnotationHub and can be retrieved directly with the AnnotationHub package. Standard GenomicFeatures accessors such as genes(), transcripts(), exonsBy(), and cdsBy() can be used to obtain gene models keyed by MSU locus identifiers. The package also provides msu_to_rap() for translating MSU locus identifiers into RAP-DB identifiers.

Author: Dwijesh Chandra Mishra [aut] ORCID iD ORCID: 0000-0002-3327-6156 , Kabilan S [aut, cre] ORCID iD ORCID: 0009-0002-9422-0938 , ICAR-IARI [fnd]

Maintainer: Kabilan S <kabilan151414 at gmail.com>

Citation (from within R, enter citation("TxDb.Osativa.MSU.RGAP7")):

Dwijesh Chandra Mishra, Kabilan S. TxDb.Osativa.MSU.RGAP7: Transcript Annotation Database for Rice. doi:10.18129/B9.bioc.TxDb.Osativa.MSU.RGAP7, R package version 0.99.10, https://bioconductor.org/packages/TxDb.Osativa.MSU.RGAP7.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("TxDb.Osativa.MSU.RGAP7")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TxDb.Osativa.MSU.RGAP7")
TxDb.Osativa.MSU.RGAP7 HTML R Script
Reference ManualPDF
NEWSText
Need some help? Ask on the Bioconductor Support site!

Details

biocViews AnnotationData, AnnotationHub, Oryza_sativa, SequenceAnnotation, TxDb
Version0.99.10
In Bioconductor sinceBioC 3.24 (R-4.6)
License Artistic-2.0
Depends R (>= 4.6.0)
Imports GenomicFeatures
System Requirements
URLhttps://github.com/kabilanbio/TxDb.Osativa.MSU.RGAP7
Bug Reportshttps://github.com/kabilanbio/TxDb.Osativa.MSU.RGAP7/issues
See More
Suggests AnnotationDbi, AnnotationHub, BiocManager, BiocStyle, Biostrings, GenomicRanges, GenomeInfoDb, knitr, riceidconverter, rmarkdown, testthat (>= 3.0.0), txdbmaker
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TxDb.Osativa.MSU.RGAP7_0.99.10.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Package Short Url https://bioconductor.org/packages/TxDb.Osativa.MSU.RGAP7/
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