Rsamtools

DOI: 10.18129/B9.bioc.Rsamtools    

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

Bioconductor version: Release (3.13)

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, Hervé Pagès, 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 "4.1") 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   Reference Manual
Text   NEWS
Text   LICENSE
Video   pileup in Rsamtools

Details

biocViews Alignment, Coverage, DataImport, QualityControl, Sequencing, Software
Version 2.8.0
In Bioconductor since BioC 2.6 (R-2.11) (11.5 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
LinkingTo Rhtslib(>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings
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
SystemRequirements GNU make
Enhances
URL https://bioconductor.org/packages/Rsamtools
BugReports https://github.com/Bioconductor/Rsamtools/issues
Depends On Me ArrayExpressHTS, BaalChIP, BitSeq, CODEX, contiBAIT, CoverageView, esATAC, exomeCopy, FRASER, GenomicAlignments, GenomicFiles, girafe, gmapR, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, r3Cseq, Rcade, RepViz, ReQON, rfPred, RiboDiPA, rnaSeqMap, SCOPE, sequencing, SGSeq, ShortRead, SICtools, SNPhood, ssviz, systemPipeR, TarSeqQC, TBX20BamSubset, TEQC, VariantAnnotation, wavClusteR
Imports Me AllelicImbalance, alpine, AneuFinder, annmap, AnnotationHubData, APAlyzer, appreci8R, ArrayExpressHTS, ASpediaFI, ASpli, ATACseqQC, BadRegionFinder, bambu, BBCAnalyzer, biovizBase, biscuiteer, breakpointR, BRGenomics, BSgenome, CAGEr, casper, cellbaseR, CexoR, ChIC, chimeraviz, ChIPComp, ChIPexoQual, ChIPpeakAnno, ChIPQC, chipseqDBData, ChIPSeqSpike, ChromSCape, chromstaR, chromVAR, cn.mops, CNVfilteR, CNVPanelizer, CNVrd2, compEpiTools, consensusDE, CopyNumberPlots, CopywriteR, CrispRVariants, csaw, CSSQ, customProDB, DAMEfinder, DegNorm, derfinder, DEXSeq, DiffBind, diffHic, easyRNASeq, EDASeq, ensembldb, epialleleR, epigenomix, epigraHMM, eudysbiome, exomePeak2, FilterFFPE, FunChIP, gcapc, GeneGeneInteR, GenoGAM, genomation, GenomicAlignments, GenomicInteractions, GenVisR, ggbio, gmoviz, GOTHiC, GreyListChIP, GUIDEseq, Gviz, h5vc, HTSeqGenie, icetea, IMAS, INSPEcT, karyoploteR, ldblock, LungCancerLines, MACPET, MADSEQ, MDTS, metagene, metagene2, metaseqR2, methylKit, MMAPPR2, MMAPPR2data, mosaics, motifmatchr, msgbsR, NADfinder, NanoMethViz, nearBynding, nucleR, ORFik, panelcn.mops, PICS, plyranges, pram, profileplyr, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, ramwas, recoup, Repitools, RiboProfiling, riboSeqR, ribosomeProfilingQC, RNAmodR, RNAprobR, RNASeqR, Rqc, rtracklayer, scruff, segmentSeq, seqplots, seqsetvis, SimFFPE, sitadela, soGGi, SplicingGraphs, srnadiff, strandCheckR, systemPipeRdata, TCseq, TFutils, tracktables, trackViewer, transcriptR, tRNAscanImport, TSRchitect, TVTB, UMI4Cats, uncoverappLib, VariantFiltering, VariantTools, VaSP, VCFArray, VplotR
Suggests Me AnnotationHub, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, Chicago, chipseqDB, epivizrChart, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gwascat, IRanges, NanoporeRNASeq, omicsPrint, parathyroidSE, RNAmodR.ML, SeqArray, seqbias, SigFuge, similaRpeak, Streamer
Links To Me
Build Report  

Package Archives

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

Source Package Rsamtools_2.8.0.tar.gz
Windows Binary Rsamtools_2.8.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) Rsamtools_2.8.0.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

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