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Bioconductor - Rsamtools

Rsamtools

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see Rsamtools.

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Bioconductor version: 3.10

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Author: Martin Morgan, Herv\'e Pag\`es, Valerie Obenchain, Nathaniel Hayden

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("Rsamtools")): Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Rsamtools")

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("Rsamtools")

Details biocViews Alignment, Coverage, DataImport, QualityControl, Sequencing, Software Version 2.2.3 In Bioconductor since BioC 2.6 (R-2.11) (14 years) License Artistic-2.0 | file LICENSE Depends methods, GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.31.8), Biostrings(>= 2.47.6) Imports utils, BiocGenerics(>= 0.25.1), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), XVector(>= 0.19.7), zlibbioc, bitops, BiocParallel System Requirements GNU make URL http://bioconductor.org/packages/Rsamtools See More Suggests GenomicAlignments, ShortRead(>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle Linking To Rhtslib(>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings Enhances Depends On Me ArrayExpressHTS, BaalChIP, BitSeq, chimera, CODEX, contiBAIT, CoverageView, esATAC, exomeCopy, GenomicAlignments, GenomicFiles, girafe, gmapR, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, r3Cseq, Rcade, RepViz, ReQON, rfPred, RIPSeeker, rnaSeqMap, sequencing, SGSeq, ShortRead, SICtools, SNPhood, ssviz, systemPipeR, TarSeqQC, TBX20BamSubset, TEQC, VariantAnnotation, wavClusteR Imports Me AllelicImbalance, alpine, AneuFinder, annmap, AnnotationHubData, appreci8R, ArrayExpressHTS, ASpediaFI, ASpli, ATACseqQC, BadRegionFinder, BBCAnalyzer, biovizBase, biscuiteer, breakpointR, BSgenome, CAGEr, casper, cellbaseR, CexoR, chimeraviz, ChIPComp, ChIPexoQual, ChIPpeakAnno, ChIPQC, ChIPSeqSpike, chromstaR, chromVAR, cn.mops, CNVfilteR, CNVPanelizer, CNVrd2, compEpiTools, consensusDE, CopyNumberPlots, CopywriteR, CrispRVariants, csaw, customProDB, derfinder, DEXSeq, DiffBind, diffHic, easyRNASeq, EDASeq, ensembldb, epigenomix, eudysbiome, FourCSeq, FunChIP, FunciSNP, gcapc, GeneGeneInteR, GenoGAM, genomation, GenomicAlignments, GenomicInteractions, GenVisR, ggbio, GGtools, GOTHiC, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, HTSeqGenie, icetea, IMAS, INSPEcT, karyoploteR, ldblock, LungCancerLines, MACPET, MADSEQ, MDTS, metagene, metagene2, methylKit, MMAPPR2, MMAPPR2data, mosaics, motifmatchr, msgbsR, MTseeker, NADfinder, ngsReports, nucleR, ORFik, panelcn.mops, PGA, PICS, plyranges, pram, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, ramwas, Rariant, Repitools, RiboProfiling, riboSeqR, RNAmodR, RNAprobR, RNASeqR, Rqc, rtracklayer, scruff, segmentSeq, seqplots, seqsetvis, soGGi, SplicingGraphs, srnadiff, strandCheckR, TCseq, TFutils, tracktables, trackViewer, transcriptR, tRNAscanImport, TSRchitect, TVTB, VariantFiltering, VariantTools, VCFArray Suggests Me AnnotationHub, APAlyzer, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, Chicago, chipseqDB, chipseqDBData, csawUsersGuide, epivizrChart, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gQTLstats, IRanges, metaseqR, omicsPrint, parathyroidSE, profileplyr, recoup, RNAmodR.ML, SeqArray, seqbias, SigFuge, similaRpeak, Streamer, TFutils Links To Me Build Report Build Report Package Archives

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

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