TxDb.Osativa.MSU.RGAP7
This is the development version of TxDb.Osativa.MSU.RGAP7; to use it, please install the devel version of Bioconductor.
Transcripts 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 is retrieved with AnnotationHub(); once loaded it can be queried with standard GenomicFeatures accessors such as genes(), transcripts(), exonsBy(), and cdsBy() 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]
, Kabilan S [aut, cre]
, ICAR-IARI [fnd]
Maintainer: Kabilan S <kabilan151414 at gmail.com>
citation("TxDb.Osativa.MSU.RGAP7")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| Transcript Annotation Database for Oryza sativa | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AnnotationData, AnnotationHub, Oryza_sativa, SequenceAnnotation, TxDb |
| Version | 0.99.9 |
| License | Artistic-2.0 |
| Depends | R (>= 4.6.0) |
| Imports | stats, GenomicFeatures, GenomicRanges, AnnotationHub |
| System Requirements | |
| URL | https://github.com/kabilanbio/TxDb.Osativa.MSU.RGAP7 |
| Bug Reports | https://github.com/kabilanbio/TxDb.Osativa.MSU.RGAP7/issues |
See More
| Suggests | BiocManager, BiocStyle, knitr, riceidconverter, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TxDb.Osativa.MSU.RGAP7_0.99.9.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/ |
| Package Downloads Report | Download Stats |