GenomicFeatures
This is the development version of GenomicFeatures; for the stable release version, see GenomicFeatures.
Query the gene models of a given organism/assembly
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version | 1.63.1 |
| In Bioconductor since | BioC 2.5 (R-2.10) (16 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
| Suggests | GenomeInfoDb, txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset(>= 0.0.5), GenomicAlignments(>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicFeatures_1.63.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |