VariantAnnotation
Annotation of Genetic Variants
Bioconductor version: 3.23 · Package version: 1.58.0
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VariantAnnotation")Details
| Maintainer | Bioconductor Package Maintainer <maintainer@bioconductor.org> |
| Author | Valerie Oberchain [aut], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb], Bioconductor Package Maintainer [cre] |
| License | Artistic-2.0 |
| System Requirements | GNU make |
| Downloads rank | 9557 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation |
Documentation
- Introduction to VariantAnnotation
- Using filterVcf() to Select Variants from VCF Files
- ensemblVEP: using the REST API with Bioconductor
Download
Dependencies
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
LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0)
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
Reverse dependencies
Depends On Me (23): alabaster.vcf, annotation, CNVrd2, deepSNV, demuxSNP, HelloRanges, myvariant, PlasmaMutationDetector, PolyPhen.Hsapiens.dbSNP131, PureCN, R453Plus1Toolbox, RareVariantVis, seqCAT, sequencing, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SomaticSignatures, StructuralVariantAnnotation, svaNUMT, VariantFiltering, variants, VariantTools, VariantToolsData
Imports Me (57): AllelicImbalance, APAlyzer, appreci8R, BadRegionFinder, BBCAnalyzer, biovizBase, biscuiteer, cardelino, CCAFE, ClonalSim, CNVfilteR, CopyNumberPlots, COSMIC.67, crisprDesign, customProDB, DAMEfinder, decompTumor2Sig, DominoEffect, fcScan, fRagmentomics, G4SNVHunter, GA4GHclient, GenomicFiles, GenVisR, ggbio, gmapR, gpcp, gwascat, gwasurvivr, icetea, igvR, karyoploteR, katdetectr, lineagespot, motifbreakR, MungeSumstats, musicatk, MutationalPatterns, MutSeqR, parati, ProteoDisco, RAIDS, scoreInvHap, SEMPLR, signeR, SigsPack, SNPhood, svaRetro, tadar, tLOH, transmogR, TVTB, Uniquorn, UPDhmm, VCFArray, YAPSA, ZygosityPredictor
Suggests Me (31): alabaster.files, AnnotationHub, AshkenazimSonChr21, BiocParallel, cellbaseR, CrispRVariants, epialleleR, GenomicDataCommons, GenomicRanges, GenomicScores, GeuvadisTranscriptExpr, GWASTools, igvShiny, ldblock, ldsep, MoBPS, omicsPrint, podkat, polyRAD, Rsamtools, RVS, SeqArray, shiny.gosling, SNPassoc, splatter, supersigs, systemPipeR, trackViewer, trio, updog, vtpnet