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Bioconductor - VariantAnnotation (development version)

VariantAnnotation

This is the development version of VariantAnnotation; for the stable release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: Development (3.22)

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 "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VariantAnnotation")

Details biocViews Annotation, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation Version 1.55.1 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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) 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 alabaster.vcf, CNVrd2, deepSNV, demuxSNP, HelloRanges, myvariant, PureCN, R453Plus1Toolbox, RareVariantVis, seqCAT, signeR, SomaticSignatures, StructuralVariantAnnotation, svaNUMT, VariantFiltering, VariantTools, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, VariantToolsData, annotation, sequencing, variants, PlasmaMutationDetector Imports Me AllelicImbalance, APAlyzer, appreci8R, BadRegionFinder, BBCAnalyzer, biovizBase, biscuiteer, cardelino, CCAFE, CNVfilteR, CopyNumberPlots, crisprDesign, customProDB, DAMEfinder, decompTumor2Sig, DominoEffect, fcScan, G4SNVHunter, GA4GHclient, GenomicFiles, GenVisR, ggbio, gmapR, gwascat, gwasurvivr, icetea, igvR, karyoploteR, katdetectr, lineagespot, motifbreakR, MungeSumstats, musicatk, MutationalPatterns, ProteoDisco, RAIDS, scoreInvHap, SigsPack, SNPhood, svaRetro, tadar, tLOH, transmogR, TVTB, Uniquorn, UPDhmm, VCFArray, YAPSA, ZygosityPredictor, COSMIC.67, gpcp Suggests Me alabaster.files, AnnotationHub, BiocParallel, cellbaseR, CrispRVariants, epialleleR, GenomicDataCommons, GenomicRanges, GenomicScores, GWASTools, igvShiny, ldblock, omicsPrint, podkat, RVS, SeqArray, shiny.gosling, splatter, supersigs, systemPipeR, trackViewer, trio, vtpnet, AshkenazimSonChr21, GeuvadisTranscriptExpr, ldsep, polyRAD, SNPassoc, updog Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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