Rsamtools
DOI:
10.18129/B9.bioc.Rsamtools
This package is for version 3.8 of Bioconductor;
for the stable, up-to-date release version, see
Rsamtools.
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Bioconductor version: 3.8
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
Author: Martin Morgan, Herv\'e Pag\`es, 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
"3.5") 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")
Details
biocViews |
Alignment, Coverage, DataImport, QualityControl, Sequencing, Software |
Version |
1.34.1 |
In Bioconductor since |
BioC 2.6 (R-2.11) (9 years) |
License |
Artistic-2.0 | file LICENSE |
Depends |
methods, GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.31.8), Biostrings(>= 2.47.6) |
Imports |
utils, BiocGenerics(>= 0.25.1), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), XVector(>= 0.19.7), zlibbioc, bitops, BiocParallel |
LinkingTo |
S4Vectors, IRanges, XVector, Biostrings |
Suggests |
GenomicAlignments, ShortRead(>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle |
SystemRequirements |
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Enhances |
|
URL |
http://bioconductor.org/packages/release/bioc/html/Rsamtools.html |
Depends On Me |
ArrayExpressHTS, BaalChIP, BitSeq, chimera, chipseqDB, CODEX, contiBAIT, CoverageView, esATAC, exomeCopy, exomePeak, GenomicAlignments, GenomicFiles, girafe, gmapR, Guitar, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, qrqc, r3Cseq, Rcade, ReQON, rfPred, RIPSeeker, rnaseqGene, rnaSeqMap, sequencing, SGSeq, ShortRead, SICtools, SNPhood, ssviz, systemPipeR, TarSeqQC, TBX20BamSubset, TEQC, VariantAnnotation, wavClusteR |
Imports Me |
AllelicImbalance, alpine, AneuFinder, annmap, AnnotationHubData, appreci8R, ArrayExpressHTS, ASpli, ATACseqQC, BadRegionFinder, BBCAnalyzer, biovizBase, breakpointR, BSgenome, CAGEr, casper, cellbaseR, CexoR, chimeraviz, ChIPComp, ChIPexoQual, ChIPpeakAnno, ChIPQC, ChIPSeqSpike, chromstaR, chromVAR, cn.mops, CNVPanelizer, CNVrd2, compEpiTools, consensusDE, CopywriteR, CrispRVariants, csaw, customProDB, derfinder, DEXSeq, DiffBind, diffHic, DOQTL, easyRNASeq, EDASeq, ensembldb, epigenomix, eudysbiome, FourCSeq, FunChIP, FunciSNP, gcapc, GeneGeneInteR, GenoGAM, genomation, GenomicAlignments, GenomicInteractions, GenVisR, ggbio, GGtools, GoogleGenomics, GOTHiC, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, HTSeqGenie, icetea, IMAS, INSPEcT, karyoploteR, ldblock, LungCancerLines, MACPET, MADSEQ, MDTS, metagene, methylKit, mosaics, motifmatchr, msgbsR, MTseeker, NADfinder, nucleR, ORFik, panelcn.mops, PGA, PICS, plyranges, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, ramwas, Rariant, Repitools, RiboProfiling, riboSeqR, RNAprobR, RNASeqR, Rqc, rtracklayer, scruff, segmentSeq, seqplots, seqsetvis, soGGi, SplicingGraphs, srnadiff, strandCheckR, TCseq, TitanCNA, tracktables, trackViewer, transcriptR, TransView, TSRchitect, TVTB, VariantFiltering, VariantTools |
Suggests Me |
AnnotationHub, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, Chicago, epivizrChart, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gQTLstats, IRanges, metaseqR, omicsPrint, parathyroidSE, recoup, SeqArray, seqbias, SigFuge, similaRpeak, Streamer, TFutils |
Links To Me |
ArrayExpressHTS, BitSeq, DiffBind, h5vc, podkat, qrqc, QuasR, seqbias, TransView, VariantAnnotation |
Build Report |
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