Rsamtools

This package is for version 3.9 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: 3.9

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")

An introduction to Rsamtools	PDF	R Script
Using samtools C libraries	PDF	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text
pileup in Rsamtools	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Coverage, DataImport, QualityControl, Sequencing, Software
Version	2.0.3
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
URL	http://bioconductor.org/packages/Rsamtools

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(>= 1.16.3), S4Vectors, IRanges, XVector, Biostrings
Enhances
Depends On Me	ArrayExpressHTS, BaalChIP, BitSeq, chimera, CODEX, contiBAIT, CoverageView, esATAC, exomeCopy, exomePeak, GenomicAlignments, GenomicFiles, girafe, gmapR, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, r3Cseq, Rcade, RepViz, ReQON, rfPred, RIPSeeker, rnaseqGene, rnaSeqMap, sequencing, SGSeq, ShortRead, SICtools, SNPhood, ssviz, systemPipeR, TarSeqQC, TBX20BamSubset, TEQC, VariantAnnotation, wavClusteR
Imports Me	AllelicImbalance, alpine, AneuFinder, annmap, AnnotationHubData, appreci8R, ArrayExpressHTS, ASpli, ATACseqQC, BadRegionFinder, BBCAnalyzer, biovizBase, breakpointR, BSgenome, CAGEr, casper, cellbaseR, CexoR, chimeraviz, ChIPComp, ChIPexoQual, ChIPpeakAnno, ChIPQC, ChIPSeqSpike, chromstaR, chromVAR, cn.mops, CNVPanelizer, CNVrd2, compEpiTools, consensusDE, CopyNumberPlots, CopywriteR, CrispRVariants, csaw, customProDB, derfinder, DEXSeq, DiffBind, diffHic, DOQTL, 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, mosaics, motifmatchr, msgbsR, MTseeker, NADfinder, ngsReports, nucleR, ORFik, panelcn.mops, PGA, PICS, plyranges, pram, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, ramwas, Rariant, Repitools, RiboProfiling, riboSeqR, RNAprobR, RNASeqR, Rqc, rtracklayer, scruff, segmentSeq, seqplots, seqsetvis, soGGi, SplicingGraphs, srnadiff, strandCheckR, TCseq, tracktables, trackViewer, transcriptR, TSRchitect, TVTB, VariantFiltering, VariantTools, VCFArray
Suggests Me	AnnotationHub, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, Chicago, chipseqDB, chipseqDBData, csawUsersGuide, epivizrChart, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gQTLstats, IRanges, metaseqR, omicsPrint, parathyroidSE, profileplyr, recoup, 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.

Source Package	Rsamtools_2.0.3.tar.gz
Windows Binary	Rsamtools_2.0.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	Rsamtools_2.0.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rsamtools
Source Repository (Developer Access)	git clone [email protected]:packages/Rsamtools
Bioc Package Browser	https://code.bioconductor.org/browse/Rsamtools/
Package Short Url	https://bioconductor.org/packages/Rsamtools/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.9	Source Archive