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VariantAnnotation
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.
Annotation of Genetic Variants
Bioconductor version: 3.6
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Author: Valerie Obenchain [aut, cre], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb]
Maintainer: Valerie Obenchain <maintainer at bioconductor.org>
Citation (from within R, enter
citation("VariantAnnotation")):
Installation
To install this package, start R (version "3.4") 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") Reference Manual
PDF
NEWS
Text
Reading VCF data
Video
Details
Version
1.24.5
In Bioconductor since
BioC 2.9 (R-2.14) (12.5 years)
License
Artistic-2.0
Depends
R (>= 2.8.0), methods, BiocGenerics(>= 0.15.3), GenomeInfoDb(>= 1.11.4), GenomicRanges(>= 1.27.6), SummarizedExperiment(>= 1.5.3), Rsamtools(>= 1.23.10)
Imports
utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.13.13), IRanges(>= 2.3.25), XVector(>= 0.5.6), Biostrings(>= 2.33.5), AnnotationDbi(>= 1.27.9), BSgenome(>= 1.37.6), rtracklayer(>= 1.25.16), GenomicFeatures(>= 1.27.4)
System Requirements
See More
Suggests
RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle
Enhances
Depends On Me
ampliQueso, cgdv17, CNVrd2, deepSNV, DOQTL, ensemblVEP, genotypeeval, GoogleGenomics, HelloRanges, HTSeqGenie, myvariant, PolyPhen.Hsapiens.dbSNP131, PureCN, R453Plus1Toolbox, RareVariantVis, Rariant, seqCAT, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SomaticSignatures, VariantFiltering, VariantTools, VariantToolsData
Imports Me
AllelicImbalance, BadRegionFinder, BBCAnalyzer, biovizBase, COSMIC.67, customProDB, FunciSNP, GA4GHclient, genbankr, GenomicFiles, ggbio, GGtools, gmapR, gQTLstats, gwascat, ldblock, MADSEQ, maftools, methyAnalysis, motifbreakR, MutationalPatterns, PGA, scoreInvHap, signeR, SNPhood, systemPipeR, TitanCNA, TVTB, YAPSA, yriMulti
Suggests Me
AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CrispRVariants, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GMRP, GWASTools, podkat, SeqArray, trackViewer, trio, vtpnet
Links To Me
Build Report
Build Report
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package
VariantAnnotation_1.24.5.tar.gz
Windows Binary
VariantAnnotation_1.24.5.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)
VariantAnnotation_1.24.5.tgz
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
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Old Source Packages for BioC 3.6
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