VariantAnnotation
This is the released version of VariantAnnotation; for the devel version, see VariantAnnotation.
Annotation of Genetic Variants
Bioconductor version: Release (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("VariantAnnotation")):
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("VariantAnnotation")
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("VariantAnnotation")| 1. Introduction to VariantAnnotation | HTML | R Script |
| 2. Using filterVcf to Select Variants from VCF Files | HTML | R Script |
| ensemblVEP: using the REST API with Bioconductor | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| - YouTube | Video |
Details
| biocViews | Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation |
| Version | 1.58.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 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
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VariantAnnotation_1.58.0.tar.gz |
| Windows Binary (x86_64) | VariantAnnotation_1.58.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | VariantAnnotation_1.58.0.tgz |
| macOS Binary (sonoma-arm64) | VariantAnnotation_1.58.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VariantAnnotation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VariantAnnotation |
| Bioc Package Browser | https://code.bioconductor.org/browse/VariantAnnotation/ |
| Package Short Url | https://bioconductor.org/packages/VariantAnnotation/ |
| Package Downloads Report | Download Stats |