Rsamtools
DOI:
10.18129/B9.bioc.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 (3.18)
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
"4.3") 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 |
2.17.0 |
In Bioconductor since |
BioC 2.6 (R-2.11) (13.5 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(>= 1.99.3), 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, knitr |
SystemRequirements |
GNU make |
Enhances |
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URL |
https://bioconductor.org/packages/Rsamtools |
BugReports |
https://github.com/Bioconductor/Rsamtools/issues |
Depends On Me |
BaalChIP, CODEX, contiBAIT, CoverageView, esATAC, exomeCopy, FRASER, GenomicAlignments, GenomicFiles, girafe, gmapR, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, r3Cseq, RepViz, ReQON, 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, 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, DegNorm, derfinder, DEXSeq, DiffBind, diffHic, DNAfusion, easyRNASeq, EDASeq, ensembldb, epigenomix, epigraHMM, eudysbiome, exomePeak2, extraChIPs, FilterFFPE, FLAMES, FunChIP, 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, metagene, metagene2, MetaScope, metaseqR2, methylKit, MMAPPR2, MMAPPR2data, mosaics, motifmatchr, msgbsR, NADfinder, NanoMethViz, nearBynding, nucleR, ORFik, panelcn.mops, PICS, plyranges, pram, profileplyr, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, ramwas, Rbowtie2, recoup, Repitools, rfPred, RiboProfiling, riboSeqR, ribosomeProfilingQC, RNAmodR, Rqc, rtracklayer, scDblFinder, scPipe, scRNAseqApp, scruff, segmentSeq, seqsetvis, SimFFPE, single, sitadela, soGGi, SplicingGraphs, srnadiff, strandCheckR, TCseq, TFutils, tracktables, trackViewer, transcriptR, TRESS, tRNAscanImport, TVTB, UMI4Cats, uncoverappLib, VariantFiltering, VariantTools, VaSP, VCFArray, VplotR, ZygosityPredictor |
Suggests Me |
AnnotationHub, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, Chicago, chipseqDB, epivizrChart, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gwascat, HIBAG, IRanges, ldblock, MungeSumstats, NanoporeRNASeq, omicsPrint, parathyroidSE, RNAmodR.ML, SeqArray, seqbias, SigFuge, similaRpeak, Streamer, systemPipeRdata, TENxIO |
Links To Me |
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Build Report |
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Package Archives
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