This package is for version 3.4 of Bioconductor;
for the stable, up-to-date release version, see
BSgenome.
Maintainer: H. Pagès <hpages at fredhutch.org>
To view documentation for the version of this package installed
in your system, start R and enter:
| biocViews |
Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching, Software |
| Version |
1.42.0 |
| In Bioconductor since |
BioC 1.9 (R-2.4) (10.5 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 2.8.0), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.9.36), IRanges(>= 2.1.33), GenomeInfoDb(>= 1.3.19), GenomicRanges(>= 1.23.15), Biostrings(>= 2.35.3), rtracklayer(>= 1.25.8) |
| Imports |
methods, utils, stats, BiocGenerics, S4Vectors, IRanges, XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer |
| LinkingTo |
|
| Suggests |
BiocInstaller, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, hgu95av2probe, RUnit |
| SystemRequirements |
|
| Enhances |
|
| URL |
|
| Depends On Me |
BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Amellifera.UCSC.apiMel2.masked, BSgenome.Athaliana.TAIR.04232008, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau3.masked, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Btaurus.UCSC.bosTau4.masked, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Btaurus.UCSC.bosTau6.masked, BSgenome.Btaurus.UCSC.bosTau8, BSgenome.Celegans.UCSC.ce10, BSgenome.Celegans.UCSC.ce11, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Cfamiliaris.UCSC.canFam2.masked, BSgenome.Cfamiliaris.UCSC.canFam3, BSgenome.Cfamiliaris.UCSC.canFam3.masked, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm2.masked, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm3.masked, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Drerio.UCSC.danRer5, BSgenome.Drerio.UCSC.danRer5.masked, BSgenome.Drerio.UCSC.danRer6, BSgenome.Drerio.UCSC.danRer6.masked, BSgenome.Drerio.UCSC.danRer7, BSgenome.Drerio.UCSC.danRer7.masked, BSgenome.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Gaculeatus.UCSC.gasAcu1.masked, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Ggallus.UCSC.galGal3.masked, BSgenome.Ggallus.UCSC.galGal4, BSgenome.Ggallus.UCSC.galGal4.masked, BSgenome.Ggallus.UCSC.galGal5, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg17.masked, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mfascicularis.NCBI.5.0, BSgenome.Mfuro.UCSC.musFur1, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac2.masked, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmulatta.UCSC.rheMac3.masked, BSgenome.Mmulatta.UCSC.rheMac8, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm8.masked, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Osativa.MSU.MSU7, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro2.masked, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Ptroglodytes.UCSC.panTro3.masked, BSgenome.Ptroglodytes.UCSC.panTro5, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Sscrofa.UCSC.susScr3, BSgenome.Sscrofa.UCSC.susScr3.masked, BSgenome.Tgondii.ToxoDB.7.0, BSgenome.Tguttata.UCSC.taeGut1, BSgenome.Tguttata.UCSC.taeGut1.masked, BSgenome.Tguttata.UCSC.taeGut2, BSgenome.Vvinifera.URGI.IGGP12Xv0, BSgenome.Vvinifera.URGI.IGGP12Xv2, BSgenome.Vvinifera.URGI.IGGP8X, CAGEr, cleanUpdTSeq, GOTHiC, HelloRanges, htSeqTools, leeBamViews, MEDIPS, motifRG, REDseq, regioneR, rGADEM, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 |
| Imports Me |
AllelicImbalance, BEAT, BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Amellifera.UCSC.apiMel2.masked, BSgenome.Athaliana.TAIR.04232008, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau3.masked, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Btaurus.UCSC.bosTau4.masked, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Btaurus.UCSC.bosTau6.masked, BSgenome.Btaurus.UCSC.bosTau8, BSgenome.Celegans.UCSC.ce10, BSgenome.Celegans.UCSC.ce11, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Cfamiliaris.UCSC.canFam2.masked, BSgenome.Cfamiliaris.UCSC.canFam3, BSgenome.Cfamiliaris.UCSC.canFam3.masked, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm2.masked, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm3.masked, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Drerio.UCSC.danRer5, BSgenome.Drerio.UCSC.danRer5.masked, BSgenome.Drerio.UCSC.danRer6, BSgenome.Drerio.UCSC.danRer6.masked, BSgenome.Drerio.UCSC.danRer7, BSgenome.Drerio.UCSC.danRer7.masked, BSgenome.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Gaculeatus.UCSC.gasAcu1.masked, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Ggallus.UCSC.galGal3.masked, BSgenome.Ggallus.UCSC.galGal4, BSgenome.Ggallus.UCSC.galGal4.masked, BSgenome.Ggallus.UCSC.galGal5, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg17.masked, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mfascicularis.NCBI.5.0, BSgenome.Mfuro.UCSC.musFur1, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac2.masked, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmulatta.UCSC.rheMac3.masked, BSgenome.Mmulatta.UCSC.rheMac8, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm8.masked, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Osativa.MSU.MSU7, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro2.masked, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Ptroglodytes.UCSC.panTro3.masked, BSgenome.Ptroglodytes.UCSC.panTro5, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Sscrofa.UCSC.susScr3, BSgenome.Sscrofa.UCSC.susScr3.masked, BSgenome.Tgondii.ToxoDB.7.0, BSgenome.Tguttata.UCSC.taeGut1, BSgenome.Tguttata.UCSC.taeGut1.masked, BSgenome.Tguttata.UCSC.taeGut2, BSgenome.Vvinifera.URGI.IGGP12Xv0, BSgenome.Vvinifera.URGI.IGGP12Xv2, BSgenome.Vvinifera.URGI.IGGP8X, charm, ChIPpeakAnno, cobindR, CRISPRseek, crisprseekplus, diffHic, fitCons.UCSC.hg19, genomation, ggbio, gmapR, GreyListChIP, GUIDEseq, Gviz, hiAnnotator, InPAS, MADSEQ, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ExAC.r0.3.1.nonTCGA.snvs.hs37d5, MafDb.ExAC.r0.3.1.snvs.hs37d5, MethylSeekR, MMDiff2, motifbreakR, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PING, podkat, qsea, QuasR, R453Plus1Toolbox, regioneR, Repitools, seqplots, signeR, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, TFBSTools, VariantAnnotation, VariantFiltering, VariantTools, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 |
| Suggests Me |
Biostrings, biovizBase, chipseq, easyRNASeq, GeneRegionScan, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, genoset, metaseqR, MiRaGE, MutationalPatterns, oneChannelGUI, QDNAseq, recoup, rtracklayer, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, spliceR, waveTiling |
| Build Report |
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