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Showing content from https://www.bioconductor.org/packages/devel/data/experiment/html/../../../bioc/html/Rsamtools.html below:

Bioconductor - Rsamtools (development version)

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 (3.22)

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 "4.5") 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")
Details biocViews Alignment, Coverage, DataImport, QualityControl, Sequencing, Software Version 2.25.1 In Bioconductor since BioC 2.6 (R-2.11) (15 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 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(>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings Enhances Depends On Me CODEX, CoverageView, esATAC, FRASER, GenomicAlignments, GenomicFiles, gmapR, HelloRanges, IntEREst, MEDIPS, methylPipe, MMDiff2, podkat, r3Cseq, RAIDS, RepViz, RiboDiPA, SCOPE, SGSeq, ShortRead, SICtools, SNPhood, spiky, ssviz, strandCheckR, systemPipeR, TEQC, VariantAnnotation, wavClusteR, leeBamViews, TBX20BamSubset, sequencing, csawBook Imports Me alabaster.files, alabaster.vcf, AllelicImbalance, annmap, AnnotationHubData, APAlyzer, appreci8R, ASpli, ATACseqQC, ATACseqTFEA, atena, BadRegionFinder, bambu, BBCAnalyzer, biovizBase, biscuiteer, breakpointR, BSgenome, CAGEr, casper, CellBarcode, cellbaseR, CexoR, cfdnakit, cfDNAPro, chimeraviz, ChIPexoQual, ChIPpeakAnno, ChIPQC, chromVAR, CircSeqAlignTk, CleanUpRNAseq, cn.mops, CNVfilteR, CNVPanelizer, CNVrd2, consensusDE, CopyNumberPlots, CrispRVariants, crupR, csaw, CSSQ, customProDB, DAMEfinder, Damsel, DegNorm, derfinder, DEXSeq, DiffBind, diffHic, DNAfusion, easyRNASeq, EDASeq, ensembldb, epigenomix, epigraHMM, eudysbiome, extraChIPs, FilterFFPE, FLAMES, gcapc, gDNAx, genomation, GenomicAlignments, GenomicInteractions, GenomicPlot, GenVisR, ggbio, gmoviz, GOTHiC, GreyListChIP, GUIDEseq, Gviz, h5vc, icetea, IMAS, INSPEcT, karyoploteR, magpie, MDTS, metagene2, metaseqR2, methylKit, mosaics, motifmatchr, MotifPeeker, msgbsR, NADfinder, NanoMethViz, nearBynding, nucleR, ORFik, panelcn.mops, PICB, plyranges, pram, profileplyr, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, raer, ramwas, Rbowtie2, recoup, Repitools, rfPred, RiboProfiling, riboSeqR, ribosomeProfilingQC, RNAmodR, Rqc, rtracklayer, scDblFinder, scPipe, scRNAseqApp, scruff, segmentSeq, seqsetvis, SimFFPE, sitadela, soGGi, SplicingGraphs, srnadiff, tadar, TCseq, TFutils, tracktables, trackViewer, transcriptR, TRESS, tRNAscanImport, TVTB, UMI4Cats, uncoverappLib, VariantFiltering, VariantTools, VaSP, VCFArray, VplotR, ZygosityPredictor, chipseqDBData, gDNAinRNAseqData, LungCancerLines, MetaScope, raerdata, BIGr, GenoPop, hoardeR, iimi, inDAGO, MAAPER, NIPTeR, noisyr, PlasmaMutationDetector, revert, scPloidy, Signac, umiAnalyzer, VALERIE Suggests Me AnnotationHub, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, BSgenomeForge, Chicago, ELViS, epivizrChart, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, gwascat, HIBAG, igvShiny, IRanges, ldblock, MOSim, MungeSumstats, omicsPrint, RNAmodR.ML, SeqArray, SigFuge, similaRpeak, Streamer, TENxIO, GeuvadisTranscriptExpr, NanoporeRNASeq, systemPipeRdata, chipseqDB, karyotapR, polyRAD, seqmagick Links To Me Build Report Build Report Package Archives

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

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