GenomicRanges
This is the released version of GenomicRanges; for the devel version, see GenomicRanges.
Representation and manipulation of genomic intervals
Bioconductor version: Release (3.23)
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.
Author: Patrick Aboyoun [aut], Hervé Pagès [aut, cre], Michael Lawrence [aut], Sonali Arora [ctb], Martin Morgan [ctb], Kayla Morrell [ctb], Valerie Obenchain [ctb], Marcel Ramos [ctb], Lori Shepherd [ctb], Dan Tenenbaum [ctb], Daniel van Twisk [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("GenomicRanges")):
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("GenomicRanges")
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("GenomicRanges")| 1. An Introduction to the GenomicRanges Package | HTML | R Script |
| 2. GenomicRanges HOWTOs | R Script | |
| 3. A quick introduction to GRanges and GRangesList objects (slides) | R Script | |
| 4. Ten Things You Didn't Know (slides from BioC 2016) | R Script | |
| 5. Extending GenomicRanges | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Coverage, DataRepresentation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version | 1.64.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (16.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0), methods, stats4, BiocGenerics(>= 0.53.2), S4Vectors(>= 0.45.2), IRanges(>= 2.43.6), Seqinfo(>= 0.99.3) |
| Imports | utils, stats |
| System Requirements | |
| URL | https://bioconductor.org/packages/GenomicRanges |
| Bug Reports | https://github.com/Bioconductor/GenomicRanges/issues |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicRanges_1.64.0.tar.gz |
| Windows Binary (x86_64) | GenomicRanges_1.64.0.zip |
| macOS Binary (big-sur-x86_64) | GenomicRanges_1.64.0.tgz |
| macOS Binary (sonoma-arm64) | GenomicRanges_1.64.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicRanges |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicRanges |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomicRanges/ |
| Package Short Url | https://bioconductor.org/packages/GenomicRanges/ |
| Package Downloads Report | Download Stats |