GenomicFeatures
This is the released version of GenomicFeatures; for the devel version, see GenomicFeatures.
Query the gene models of a given organism/assembly
Bioconductor version: Release (3.23)
Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.
Author: H. Pagès [aut, cre], M. Carlson [aut], P. Aboyoun [aut], S. Falcon [aut], M. Morgan [aut], D. Sarkar [aut], M. Lawrence [aut], V. Obenchain [aut], S. Arora [ctb], J. MacDonald [ctb], M. Ramos [ctb], S. Saini [ctb], P. Shannon [ctb], L. Shepherd [ctb], D. Tenenbaum [ctb], D. Van Twisk [ctb]
Maintainer: H. Pagès <hpages.on.github at gmail.com>
citation("GenomicFeatures")):
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")
BiocManager::install("GenomicFeatures")
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("GenomicFeatures")| Obtaining and Utilizing TxDb Objects | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version | 1.64.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (17 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), BiocGenerics(>= 0.51.2), S4Vectors(>= 0.47.6), IRanges(>= 2.37.1), Seqinfo(>= 0.99.2), GenomicRanges(>= 1.61.1), AnnotationDbi(>= 1.41.4) |
| Imports | methods, utils, stats, DBI, XVector, Biostrings(>= 2.77.2), rtracklayer(>= 1.69.1) |
| System Requirements | |
| URL | https://bioconductor.org/packages/GenomicFeatures |
| Bug Reports | https://github.com/Bioconductor/GenomicFeatures/issues |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicFeatures_1.64.0.tar.gz |
| Windows Binary (x86_64) | GenomicFeatures_1.64.0.zip |
| macOS Binary (big-sur-x86_64) | GenomicFeatures_1.64.0.tgz |
| macOS Binary (sonoma-arm64) | GenomicFeatures_1.64.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicFeatures |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicFeatures |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomicFeatures/ |
| Package Short Url | https://bioconductor.org/packages/GenomicFeatures/ |
| Package Downloads Report | Download Stats |