Rsamtools

DOI: 10.18129/B9.bioc.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 (!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 2.2.3
In Bioconductor since BioC 2.6 (R-2.11) (10 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 Rhtslib(>= 1.17.7), 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 GNU make
Enhances
URL http://bioconductor.org/packages/Rsamtools
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  

Package Archives

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

Source Package Rsamtools_2.2.3.tar.gz
Windows Binary Rsamtools_2.2.3.zip
Mac OS X 10.11 (El Capitan) Rsamtools_2.2.3.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 https://bioconductor.org/packages/Rsamtools/
Package Downloads Report Download Stats

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