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>

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

Installation

To install this package, start R (version "3.5") 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 1.34.1

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/release/bioc/html/Rsamtools.html

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 S4Vectors, IRanges, XVector, Biostrings

Enhances

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

Links To Me ArrayExpressHTS, BitSeq, DiffBind, h5vc, podkat, qrqc, QuasR, seqbias, TransView, VariantAnnotation

Build Report 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

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 3.8 Source Archive