Rsamtools

This is the development version of Rsamtools; for the stable release version, see Rsamtools.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6

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

Bioconductor version: Development (3.24)

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, enter citation("Rsamtools")):

Martin Morgan, Hervé Pagès, Valerie Obenchain, Nathaniel Hayden. Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. doi:10.18129/B9.bioc.Rsamtools, R package version 2.29.0, https://bioconductor.org/packages/Rsamtools.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text
Video	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Coverage, DataImport, QualityControl, Sequencing, Software
Version	2.29.0
In Bioconductor since	BioC 2.6 (R-2.11) (16.5 years)
License	Artistic-2.0 \| file LICENSE
Depends	R (>= 3.5.0), methods, Seqinfo, GenomicRanges (>= 1.61.1), Biostrings (>= 2.77.2)
Imports	utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops, BiocParallel, stats
System Requirements	GNU make
URL	https://bioconductor.org/packages/Rsamtools
Bug Reports	https://github.com/Bioconductor/Rsamtools/issues

Suggests	GenomicAlignments, 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 To	Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings
Enhances
Depends On Me	BaalChIP, CODEX, CoverageView, csawBook, esATAC, FRASER, GenomicAlignments, GenomicFiles, gmapR, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, r3Cseq, RAIDS, RepViz, RiboDiPA, SCOPE, sequencing, SGSeq, ShortRead, SICtools, SNPhood, spiky, ssviz, strandCheckR, systemPipeR, TBX20BamSubset, TEQC, VariantAnnotation, wavClusteR
Imports Me	alabaster.files, alabaster.vcf, AllelicImbalance, annmap, AnnotationHubData, appreci8R, ASpli, ATACseqQC, ATACseqTFEA, atena, BadRegionFinder, bambu, BamScale, BBCAnalyzer, BIGr, Bioc.gff, biovizBase, biscuiteer, breakpointR, BSgenome, CAGEr, casper, CellBarcode, cellbaseR, CexoR, cfdnakit, cfDNAPro, chimeraviz, ChIPexoQual, ChIPpeakAnno, ChIPQC, chipseqDBData, ChromSCape, chromVAR, CircSeqAlignTk, CleanUpRNAseq, cn.mops, CNVfilteR, CNVPanelizer, CNVrd2, compEpiTools, CopyNumberPlots, CrispRVariants, crupR, csaw, CSSQ, customProDB, DAMEfinder, Damsel, dbSequence, DegNorm, derfinder, DEXSeq, DiffBind, diffHic, DMRcaller, DNAfusion, DOTSeq, easyRNASeq, EDASeq, ensembldb, epigenomix, epigraHMM, eudysbiome, EventPointer, extraChIPs, FilterFFPE, FLAMES, fRagmentomics, gcapc, gDNAinRNAseqData, gDNAx, genomation, GenomicInteractions, GenomicPlot, GenoPop, GenVisR, ggbio, gmoviz, GOTHiC, GreyListChIP, GUIDEseq, Gviz, h5vc, icetea, iimi, ImprintCapASM, INSPEcT, karyoploteR, LungCancerLines, magpie, MDTS, metagene2, MetaScope, metaseqR2, methylKit, MitoHEAR, mosaics, motifmatchr, MotifPeeker, msgbsR, NADfinder, NanoMethViz, NGSToolKit, NIPTeR, noisyr, nucleR, ORFik, panelcn.mops, PICB, PlasmaMutationDetector, plyranges, pram, profileplyr, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, raer, raerdata, ramwas, Rbowtie2, recoup, revert, rfPred, riboSeqR, ribosomeProfilingQC, RNAmodR, RNAshapeQC, Rqc, rtracklayer, scDblFinder, scPipe, scPloidy, scRNAseqApp, scruff, segmentSeq, seqsetvis, Signac, SimFFPE, sitadela, SplicingGraphs, srnadiff, tadar, TCseq, TFutils, tracktables, trackViewer, transcriptR, TRESS, tRNAscanImport, TSSr, TVTB, UMI4Cats, umiAnalyzer, uncoverappLib, VALERIE, VariantFiltering, VariantTools, VCFArray, VplotR, ZygosityPredictor
Suggests Me	AnnotationHub, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, BSgenomeForge, Chicago, chipseqDB, cigarillo, ELViS, epivizrChart, futurize, gaawr2, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gwascat, HIBAG, igvShiny, inDAGO, IRanges, iscream, karyotapR, ldblock, MoBPS, MOSim, MungeSumstats, NanoporeRNASeq, omicsPrint, polyRAD, RNAmodR.ML, seqmagick, similaRpeak, systemPipeRdata, TENxIO
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	Rsamtools_2.29.0.tar.gz
Windows Binary (x86_64)	Rsamtools_2.29.0.zip
macOS Binary (big-sur-x86_64)	Rsamtools_2.29.0.tgz
macOS Binary (sonoma-arm64)	Rsamtools_2.29.0.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