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.
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biocViews |
Alignment, Coverage, DataImport, QualityControl, Sequencing, Software |
Version |
2.4.0 |
In Bioconductor since |
BioC 2.6 (R-2.11) (10.5 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, stats |
LinkingTo |
Rhtslib(>= 1.17.7), 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 |
GNU make |
Enhances |
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URL |
http://bioconductor.org/packages/Rsamtools |
Depends On Me |
ArrayExpressHTS, BaalChIP, BitSeq, chimera, CODEX, contiBAIT, CoverageView, esATAC, exomeCopy, FRASER, GenomicAlignments, GenomicFiles, girafe, gmapR, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, r3Cseq, Rcade, RepViz, ReQON, rfPred, RIPSeeker, rnaSeqMap, SCOPE, sequencing, SGSeq, ShortRead, SICtools, SNPhood, ssviz, systemPipeR, TarSeqQC, TBX20BamSubset, TEQC, VariantAnnotation, wavClusteR |
Imports Me |
AllelicImbalance, alpine, AneuFinder, annmap, AnnotationHubData, appreci8R, ArrayExpressHTS, ASpediaFI, ASpli, ATACseqQC, BadRegionFinder, BBCAnalyzer, biovizBase, biscuiteer, breakpointR, BRGenomics, BSgenome, CAGEr, casper, cellbaseR, CexoR, chimeraviz, ChIPComp, ChIPexoQual, ChIPpeakAnno, ChIPQC, ChIPSeqSpike, chromstaR, chromVAR, cn.mops, CNVfilteR, CNVPanelizer, CNVrd2, compEpiTools, consensusDE, CopyNumberPlots, CopywriteR, CrispRVariants, csaw, CSSQ, customProDB, DAMEfinder, derfinder, DEXSeq, DiffBind, diffHic, easyRNASeq, EDASeq, ensembldb, epigenomix, eudysbiome, exomePeak2, FourCSeq, FunChIP, FunciSNP, gcapc, GeneGeneInteR, GenoGAM, genomation, GenomicAlignments, GenomicInteractions, GenVisR, ggbio, GGtools, gmoviz, GOTHiC, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, HTSeqGenie, icetea, IMAS, INSPEcT, karyoploteR, ldblock, LungCancerLines, MACPET, MADSEQ, MDTS, metagene, metagene2, metaseqR2, methylKit, MMAPPR2, MMAPPR2data, mosaics, motifmatchr, msgbsR, MTseeker, NADfinder, ngsReports, nucleR, ORFik, panelcn.mops, PGA, PICS, plyranges, pram, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, ramwas, Rariant, Repitools, RiboProfiling, riboSeqR, ribosomeProfilingQC, RNAmodR, RNAprobR, RNASeqR, Rqc, rtracklayer, scruff, segmentSeq, seqplots, seqsetvis, SimFFPE, soGGi, SplicingGraphs, srnadiff, strandCheckR, TCseq, TFutils, tracktables, trackViewer, transcriptR, tRNAscanImport, TSRchitect, TVTB, VariantFiltering, VariantTools, vasp, VCFArray |
Suggests Me |
AnnotationHub, APAlyzer, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, Chicago, chipseqDB, chipseqDBData, csawUsersGuide, epivizrChart, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gQTLstats, IRanges, metaseqR, omicsPrint, parathyroidSE, profileplyr, recoup, RNAmodR.ML, SeqArray, seqbias, SigFuge, similaRpeak, Streamer, TFutils |
Links To Me |
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Build Report |
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