Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Bioconductor version: 3.23 · Package version: 2.28.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rsamtools")Details
| Maintainer | Bioconductor Package Maintainer <maintainer@bioconductor.org> |
| 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] |
| License | Artistic-2.0 | file LICENSE |
| URL | https://bioconductor.org/packages/Rsamtools |
| Bug Reports | https://github.com/Bioconductor/Rsamtools/issues |
| System Requirements | GNU make |
| Downloads rank | 29790 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, Coverage, DataImport, QualityControl, Sequencing, Software |
Documentation
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Dependencies
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
LinkingTo: Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings
Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, VariantAnnotation, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr
Reverse dependencies
Depends On Me (33): BaalChIP, CODEX, CoverageView, esATAC, FRASER, GenomicAlignments, GenomicFiles, gmapR, HelloRanges, IntEREst, leeBamViews, MEDIPS, methylPipe, MMDiff2, podkat, r3Cseq, RAIDS, RepViz, RiboDiPA, SCOPE, sequencing, SGSeq, ShortRead, SICtools, SNPhood, spiky, ssviz, strandCheckR, systemPipeR, TBX20BamSubset, TEQC, VariantAnnotation, wavClusteR
Imports Me (166): alabaster.files, alabaster.vcf, AllelicImbalance, annmap, AnnotationHubData, APAlyzer, appreci8R, ASpli, ATACseqQC, ATACseqTFEA, atena, BadRegionFinder, bambu, BBCAnalyzer, BIGr, Bioc.gff, biovizBase, biscuiteer, breakpointR, BSgenome, CAGEr, casper, CellBarcode, cellbaseR, CexoR, cfdnakit, cfDNAPro, chimeraviz, ChIPComp, ChIPexoQual, ChIPpeakAnno, ChIPQC, chipseqDBData, ChromSCape, chromVAR, CircSeqAlignTk, CleanUpRNAseq, cn.mops, CNVfilteR, CNVPanelizer, CNVrd2, compEpiTools, CopyNumberPlots, CrispRVariants, crupR, csaw, CSSQ, customProDB, DAMEfinder, Damsel, DegNorm, derfinder, DEXSeq, DiffBind, diffHic, DMRcaller, DNAfusion, DOTSeq, easyRNASeq, EDASeq, ensembldb, epigenomix, epigraHMM, eudysbiome, EventPointer, extraChIPs, FilterFFPE, FLAMES, fRagmentomics, gcapc, gDNAinRNAseqData, gDNAx, genomation, GenomicAlignments, GenomicInteractions, GenomicPlot, GenoPop, GenVisR, ggbio, gmoviz, GOTHiC, GreyListChIP, GUIDEseq, Gviz, h5vc, icetea, iimi, IMAS, ImprintCapASM, INSPEcT, karyoploteR, LungCancerLines, magpie, MDTS, metagene2, MetaScope, metaseqR2, methylKit, MitoHEAR, mosaics, motifmatchr, MotifPeeker, msgbsR, NADfinder, NanoMethViz, NIPTeR, noisyr, nucleR, ORFik, panelcn.mops, PICB, PlasmaMutationDetector, plyranges, pram, profileplyr, PureCN, QDNAseq, qsea, QuasR, R453Plus1Toolbox, raer, raerdata, ramwas, Rbowtie2, recoup, revert, rfPred, RiboProfiling, riboSeqR, ribosomeProfilingQC, RNAmodR, RNAshapeQC, Rqc, rtracklayer, scDblFinder, scPipe, scPloidy, scRNAseqApp, scruff, segmentSeq, seqsetvis, Signac, SimFFPE, sitadela, soGGi, SplicingGraphs, srnadiff, tadar, TCseq, TFutils, tracktables, trackViewer, transcriptR, TRESS, tRNAscanImport, TVTB, UMI4Cats, umiAnalyzer, uncoverappLib, VALERIE, VariantFiltering, VariantTools, VaSP, VCFArray, VplotR, ZygosityPredictor
Suggests Me (41): AnnotationHub, bamsignals, BaseSpaceR, BiocGenerics, BiocParallel, biomvRCNS, BSgenomeForge, Chicago, chipseqDB, cigarillo, ELViS, epivizrChart, futurize, gaawr2, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GeuvadisTranscriptExpr, gwascat, HIBAG, igvShiny, inDAGO, IRanges, iscream, karyotapR, ldblock, MoBPS, MOSim, MungeSumstats, NanoporeRNASeq, omicsPrint, polyRAD, RNAmodR.ML, SeqArray, seqmagick, SigFuge, similaRpeak, systemPipeRdata, TENxIO