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Rsamtools

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

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


Bioconductor version: Development (3.20)

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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
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
pileup in Rsamtools Video

Details

biocViews Alignment, Coverage, DataImport, QualityControl, Sequencing, Software
Version 2.21.0
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), R (>= 3.5.0)
Imports utils, BiocGenerics(>= 0.25.1), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), XVector(>= 0.19.7), zlibbioc, bitops, BiocParallel, stats
System Requirements GNU make
URL https://bioconductor.org/packages/Rsamtools
Bug Reports https://github.com/Bioconductor/Rsamtools/issues
See More
Suggests GenomicAlignments, ShortRead(>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr
Linking To Rhtslib(>= 2.99.1), S4Vectors, IRanges, XVector, Biostrings
Enhances
Depends On Me BaalChIP, CODEX, CoverageView, esATAC, FRASER, GenomicAlignments, GenomicFiles, girafe, gmapR, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, r3Cseq, RepViz, RiboDiPA, SCOPE, sequencing, SGSeq, ShortRead, SICtools, SNPhood, spiky, ssviz, systemPipeR, TBX20BamSubset, TEQC, VariantAnnotation, wavClusteR
Imports Me alabaster.files, alabaster.vcf, AllelicImbalance, AneuFinder, annmap, AnnotationHubData, APAlyzer, appreci8R, ASpli, ATACseqQC, ATACseqTFEA, atena, BadRegionFinder, bambu, BBCAnalyzer, biovizBase, biscuiteer, breakpointR, BRGenomics, BSgenome, CAGEr, casper, CellBarcode, cellbaseR, CexoR, cfdnakit, cfDNAPro, chimeraviz, ChIPComp, ChIPexoQual, ChIPpeakAnno, ChIPQC, chipseqDBData, ChromSCape, chromstaR, chromVAR, CircSeqAlignTk, cn.mops, CNVfilteR, CNVPanelizer, CNVrd2, compEpiTools, consensusDE, CopyNumberPlots, CrispRVariants, csaw, CSSQ, customProDB, DAMEfinder, Damsel, DegNorm, derfinder, DEXSeq, DiffBind, diffHic, DNAfusion, easyRNASeq, EDASeq, ensembldb, epigenomix, epigraHMM, eudysbiome, extraChIPs, FilterFFPE, FLAMES, gcapc, gDNAinRNAseqData, gDNAx, GeneGeneInteR, genomation, GenomicAlignments, GenomicInteractions, GenomicPlot, GenVisR, ggbio, gmoviz, GOTHiC, GreyListChIP, GUIDEseq, Gviz, h5vc, HTSeqGenie, icetea, IMAS, INSPEcT, karyoploteR, LungCancerLines, MADSEQ, magpie, MDTS, metagene2, MetaScope, metaseqR2, methylKit, mosaics, motifmatchr, msgbsR, NADfinder, NanoMethViz, nearBynding, nucleR, ORFik, panelcn.mops, PICS, plyranges, pram, profileplyr, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, raer, raerdata, ramwas, Rbowtie2, recoup, Repitools, rfPred, RiboProfiling, riboSeqR, ribosomeProfilingQC, RNAmodR, Rqc, rtracklayer, scDblFinder, scPipe, scRNAseqApp, scruff, segmentSeq, seqsetvis, SimFFPE, single, sitadela, soGGi, SplicingGraphs, srnadiff, strandCheckR, tadar, TCseq, TFutils, tracktables, trackViewer, transcriptR, TRESS, tRNAscanImport, TVTB, UMI4Cats, uncoverappLib, VariantFiltering, VariantTools, VaSP, VCFArray, VplotR, ZygosityPredictor
Suggests Me AnnotationHub, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, BSgenomeForge, Chicago, chipseqDB, epivizrChart, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gwascat, HIBAG, igvShiny, IRanges, ldblock, MOSim, MungeSumstats, NanoporeRNASeq, omicsPrint, parathyroidSE, RNAmodR.ML, SeqArray, SigFuge, similaRpeak, Streamer, systemPipeRdata, TENxIO
Links To Me
Build Report Build Report

Package Archives

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

Source Package Rsamtools_2.21.0.tar.gz
Windows Binary Rsamtools_2.21.0.zip (64-bit only)
macOS Binary (x86_64) Rsamtools_2.21.0.tgz
macOS Binary (arm64) Rsamtools_2.21.0.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