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Rsamtools

This is thereleased version of Rsamtools; for the devel version, seeRsamtools.

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

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DOI: 10.18129/B9.bioc.Rsamtools


Bioconductor version: Release (3.22)

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 [aut], Hervé Pagès [aut], Valerie Obenchain [aut], Nathaniel Hayden [aut], Busayo Samuel [ctb] (Converted Rsamtools vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre]

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

Citation (from within R, entercitation("Rsamtools")):

Installation

To install this package, start R (version "4.5") and enter:

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

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

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

browseVignettes("Rsamtools")
An Introduction to RsamtoolsHTMLR Script
Reference ManualPDF
NEWSText
LICENSEText
Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViewsAlignment,Coverage,DataImport,QualityControl,Sequencing,Software
Version2.26.0
In Bioconductor sinceBioC 2.6 (R-2.11) (15.5 years)
LicenseArtistic-2.0 | fileLICENSE
DependsR (>= 3.5.0), methods,Seqinfo,GenomicRanges(>= 1.61.1),Biostrings(>= 2.77.2)
Importsutils,BiocGenerics(>= 0.25.1),S4Vectors(>= 0.17.25),IRanges(>= 2.13.12),XVector(>= 0.19.7),bitops,BiocParallel, stats
System RequirementsGNU make
URLhttps://bioconductor.org/packages/Rsamtools
Bug Reportshttps://github.com/Bioconductor/Rsamtools/issues
See More
SuggestsGenomicAlignments,ShortRead(>= 1.19.10),GenomicFeatures,VariantAnnotation,TxDb.Dmelanogaster.UCSC.dm3.ensGene,TxDb.Hsapiens.UCSC.hg18.knownGene,RNAseqData.HNRNPC.bam.chr14,BSgenome.Hsapiens.UCSC.hg19,RUnit,BiocStyle,knitr
Linking ToRhtslib(>= 3.3.1),S4Vectors,IRanges,XVector,Biostrings
Enhances
Depends On MeCODEX,CoverageView,esATAC,FRASER,GenomicAlignments,GenomicFiles,gmapR,HelloRanges,IntEREst,MEDIPS,methylPipe,MMDiff2,podkat,r3Cseq,RAIDS,RiboDiPA,SCOPE,SGSeq,ShortRead,SICtools,SNPhood,spiky,ssviz,strandCheckR,systemPipeR,TEQC,VariantAnnotation,wavClusteR,leeBamViews,TBX20BamSubset,sequencing, csawBook
Imports Mealabaster.files,alabaster.vcf,AllelicImbalance,annmap,AnnotationHubData,appreci8R,ASpli,ATACseqQC,ATACseqTFEA,atena,BadRegionFinder,bambu,BBCAnalyzer,Bioc.gff,biovizBase,biscuiteer,breakpointR,BSgenome,CAGEr,casper,CellBarcode,cellbaseR,CexoR,cfdnakit,cfDNAPro,chimeraviz,ChIPexoQual,ChIPpeakAnno,ChromSCape,chromVAR,CircSeqAlignTk,CleanUpRNAseq,cn.mops,CNVfilteR,CNVPanelizer,CNVrd2,compEpiTools,consensusDE,CopyNumberPlots,CrispRVariants,crupR,csaw,CSSQ,DAMEfinder,Damsel,DegNorm,derfinder,DEXSeq,DiffBind,diffHic,DMRcaller,DNAfusion,easyRNASeq,EDASeq,ensembldb,epigraHMM,eudysbiome,extraChIPs,FilterFFPE,FLAMES,gcapc,gDNAx,genomation,GenomicAlignments,GenomicInteractions,GenomicPlot,ggbio,gmoviz,GOTHiC,GreyListChIP,GUIDEseq,Gviz,h5vc,icetea,INSPEcT,karyoploteR,magpie,MDTS,metagene2,metaseqR2,methylKit,mosaics,motifmatchr,MotifPeeker,msgbsR,NADfinder,NanoMethViz,nearBynding,nucleR,ORFik,panelcn.mops,PICB,plyranges,pram,PureCN,QDNAseq,qsea,QuasR,raer,ramwas,Rbowtie2,recoup,rfPred,RiboProfiling,riboSeqR,ribosomeProfilingQC,RNAmodR,Rqc,rtracklayer,scDblFinder,scPipe,scRNAseqApp,scruff,segmentSeq,seqsetvis,SimFFPE,sitadela,SplicingGraphs,srnadiff,tadar,TCseq,TFutils,tracktables,trackViewer,transcriptR,TRESS,tRNAscanImport,TVTB,UMI4Cats,uncoverappLib,VariantFiltering,VariantTools,VaSP,VCFArray,VplotR,ZygosityPredictor,chipseqDBData,gDNAinRNAseqData,LungCancerLines,MetaScope,raerdata,BIGr,GenoPop,hoardeR,iimi,MAAPER,NIPTeR,noisyr,PlasmaMutationDetector,revert,scPloidy,Signac,umiAnalyzer,VALERIE
Suggests MeAnnotationHub,bamsignals,BaseSpaceR,BiocGenerics,BiocParallel,biomvRCNS,BSgenomeForge,Chicago,cigarillo,ELViS,epivizrChart,gage,GenomeInfoDb,GenomicDataCommons,GenomicFeatures,GenomicRanges,gwascat,HIBAG,igvShiny,IRanges,iscream,ldblock,MOSim,MungeSumstats,omicsPrint,RNAmodR.ML,SeqArray,similaRpeak,Streamer,TENxIO,GeuvadisTranscriptExpr,NanoporeRNASeq,systemPipeRdata,chipseqDB,inDAGO,karyotapR,MoBPS,polyRAD,seqmagick
Links To Me
Build ReportBuild Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source PackageRsamtools_2.26.0.tar.gz
Windows Binary (x86_64) Rsamtools_2.26.0.zip (64-bit only)
macOS Binary (x86_64)Rsamtools_2.26.0.tgz
macOS Binary (arm64)Rsamtools_2.26.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/Rsamtools
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/Rsamtools
Bioc Package Browserhttps://code.bioconductor.org/browse/Rsamtools/
Package Short Urlhttps://bioconductor.org/packages/Rsamtools/
Package Downloads ReportDownload Stats
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