VariantAnnotation
This is the development version of VariantAnnotation; for the stable release version, see VariantAnnotation.
Annotation of Genetic Variants
Bioconductor version: Development (3.23)
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Author: Valerie Oberchain [aut], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb], Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation (from within R, enter
citation("VariantAnnotation")):
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("VariantAnnotation")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| Video |
Details
| biocViews | Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation |
| Version | 1.57.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (14 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0), methods, BiocGenerics(>= 0.37.0), MatrixGenerics, Seqinfo, GenomicRanges(>= 1.61.1), SummarizedExperiment(>= 1.39.1), Rsamtools(>= 2.25.1) |
| Imports | utils, DBI, Biobase, S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), XVector(>= 0.29.2), Biostrings(>= 2.77.2), AnnotationDbi(>= 1.27.9), rtracklayer(>= 1.69.1), BSgenome(>= 1.77.1), GenomicFeatures(>= 1.61.4), curl |
| System Requirements | GNU make |
| URL |
See More
| Suggests | GenomeInfoDb, RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons |
| Linking To | S4Vectors, IRanges, XVector, Biostrings, Rhtslib(>= 2.99.0) |
| 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/VariantAnnotation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VariantAnnotation |
| Package Short Url | https://bioconductor.org/packages/VariantAnnotation/ |
| Package Downloads Report | Download Stats |