Rsamtools

DOI: 10.18129/B9.bioc.Rsamtools    

This package is for version 3.8 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: 3.8

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') 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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Alignment, Coverage, DataImport, QualityControl, Sequencing, Software
Version	1.34.1
In Bioconductor since	BioC 2.6 (R-2.11) (9 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
LinkingTo	S4Vectors, IRanges, XVector, Biostrings
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
SystemRequirements
Enhances
URL	http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Depends On Me	ArrayExpressHTS, BaalChIP, BitSeq, chimera, chipseqDB, CODEX, contiBAIT, CoverageView, esATAC, exomeCopy, exomePeak, GenomicAlignments, GenomicFiles, girafe, gmapR, Guitar, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, qrqc, r3Cseq, Rcade, 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, 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, GoogleGenomics, GOTHiC, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, HTSeqGenie, icetea, IMAS, INSPEcT, karyoploteR, ldblock, LungCancerLines, MACPET, MADSEQ, MDTS, metagene, methylKit, mosaics, motifmatchr, msgbsR, MTseeker, NADfinder, nucleR, ORFik, panelcn.mops, PGA, PICS, plyranges, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, ramwas, Rariant, Repitools, RiboProfiling, riboSeqR, RNAprobR, RNASeqR, Rqc, rtracklayer, scruff, segmentSeq, seqplots, seqsetvis, soGGi, SplicingGraphs, srnadiff, strandCheckR, TCseq, TitanCNA, tracktables, trackViewer, transcriptR, TransView, TSRchitect, TVTB, VariantFiltering, VariantTools
Suggests Me	AnnotationHub, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, Chicago, epivizrChart, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gQTLstats, IRanges, metaseqR, omicsPrint, parathyroidSE, recoup, SeqArray, seqbias, SigFuge, similaRpeak, Streamer, TFutils
Links To Me	ArrayExpressHTS, BitSeq, DiffBind, h5vc, podkat, qrqc, QuasR, seqbias, TransView, VariantAnnotation
Build Report

Package Archives

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

Source Package	Rsamtools_1.34.1.tar.gz
Windows Binary	Rsamtools_1.34.1.zip
Mac OS X 10.11 (El Capitan)	Rsamtools_1.34.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rsamtools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Rsamtools
Package Short Url	http://bioconductor.org/packages/Rsamtools/
Package Downloads Report	Download Stats