GenomicRanges
This is the development version of GenomicRanges; for the stable release version, see GenomicRanges.
Representation and manipulation of genomic intervals
Bioconductor version: Development (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")):
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("GenomicRanges")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Annotation, Coverage, DataRepresentation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version | 1.63.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (15.5 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
| Suggests | GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings(>= 2.77.2), SummarizedExperiment(>= 1.39.1), Rsamtools, GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle |
| Linking To | S4Vectors, IRanges |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicRanges |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicRanges |
| Package Short Url | https://bioconductor.org/packages/GenomicRanges/ |
| Package Downloads Report | Download Stats |