BSgenome

DOI:10.18129 / B9.bioc.BSgenome

这个包是3.11版本Bioconductor;的稳定,最新的发布版本,请参阅BSgenome

软件基础设施的有效表示完整的基因组及其单核苷酸多态性

Bioconductor版本:3.11

基础设施由所有Biostrings-based基因组数据共享包。

作者:Herve页面

维修工:h .页< hpages fredhutch.org >

从内部引用(R,回车引用(“BSgenome”)):

安装

安装这个包,开始R(版本“4.0”)并输入:

如果(!requireNamespace (“BiocManager”,悄悄地= TRUE)) install.packages (“BiocManager”) BiocManager::安装(“BSgenome”)

R的旧版本,请参考适当的Bioconductor释放

文档

查看文档的版本这个包安装在您的系统,开始R和输入:

browseVignettes (“BSgenome”)

PDF R脚本 高效的基因组搜索与Biostrings BSgenome包数据
PDF R脚本 如何打造一个BSgenome数据包
PDF 参考手册
文本 新闻

细节

biocViews 注释,DataRepresentation,遗传学,基础设施,单核苷酸多态性,SequenceMatching,软件
版本 1.56.0
Bioconductor自 BioC 1.9 (r - 2.4)(14年)
许可证 艺术- 2.0
取决于 R(> = 2.8.0)、方法BiocGenerics(> = 0.13.8),S4Vectors(> = 0.17.28),IRanges(> = 2.13.16),GenomeInfoDb(> = 1.23.9),GenomicRanges(> = 1.31.10),Biostrings(> = 2.47.6),rtracklayer(> = 1.39.7)
进口 方法,跑龙套,统计数据,matrixStats,BiocGenerics,S4Vectors,IRanges,XVector,GenomeInfoDb,GenomicRanges,Biostrings,Rsamtools,rtracklayer
链接
建议 BiocManager,Biobase,BSgenome.Celegans.UCSC.ce2,BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38.masked,BSgenome.Mmusculus.UCSC.mm10,BSgenome.Rnorvegicus.UCSC.rn5,BSgenome.Scerevisiae.UCSC.sacCer1,BSgenome.Hsapiens.NCBI.GRCh38,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene,SNPlocs.Hsapiens.dbSNP144.GRCh38,XtraSNPlocs.Hsapiens.dbSNP144.GRCh38,hgu95av2probe,RUnit
SystemRequirements
增强了
URL
取决于我 注释,BSgenome.Alyrata.JGI.v1,BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked,BSgenome.Aofficinalis.NCBI.V1,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.Btaurus.UCSC.bosTau9,BSgenome.Carietinum.NCBI.v1,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.Cjacchus.UCSC.calJac3,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.danRer11,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.Dvirilis.Ensembl.dvircaf1,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.Ggallus.UCSC.galGal6,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.Mdomestica.UCSC.monDom5,BSgenome.Mfascicularis.NCBI.5.0,BSgenome.Mfuro.UCSC.musFur1,BSgenome.Mmulatta.UCSC.rheMac10,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.Ptroglodytes.UCSC.panTro6,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.susScr11,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,ChIPanalyser,哥特,HelloRanges,leeBamViews,MEDIPS,motifRG,REDseq,rGADEM,SNPlocs.Hsapiens.dbSNP.20120608,SNPlocs.Hsapiens.dbSNP141.GRCh38,SNPlocs.Hsapiens.dbSNP142.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh38,SNPlocs.Hsapiens.dbSNP149.GRCh38,SNPlocs.Hsapiens.dbSNP150.GRCh38,SNPlocs.Hsapiens.dbSNP151.GRCh38,XtraSNPlocs.Hsapiens.dbSNP141.GRCh38,XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
进口我 AllelicImbalance,appreci8R,ATACseqQC,atSNP,击败,BSgenome.Alyrata.JGI.v1,BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked,BSgenome.Aofficinalis.NCBI.V1,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.Btaurus.UCSC.bosTau9,BSgenome.Carietinum.NCBI.v1,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.Cjacchus.UCSC.calJac3,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.danRer11,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.Dvirilis.Ensembl.dvircaf1,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.Ggallus.UCSC.galGal6,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.Mdomestica.UCSC.monDom5,BSgenome.Mfascicularis.NCBI.5.0,BSgenome.Mfuro.UCSC.musFur1,BSgenome.Mmulatta.UCSC.rheMac10,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.Ptroglodytes.UCSC.panTro6,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.susScr11,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,bsseq,BUSpaRse,篮球选手,ChIPpeakAnno,chromVAR,circRNAprofiler,cleanUpdTSeq,cobindR,CRISPRseek,crisprseekplus,diffHic,dpeak,enrichTF,esATAC,EventPointer,exomePeak2,fitCons.UCSC.hg19,弗雷泽,gcapc,genomation,GenVisR,ggbio,gmapR,GreyListChIP,GUIDEseq,Gviz,hiAnnotator,InPAS,IsoformSwitchAnalyzeR,MADSEQ,MafDb.1Kgenomes.phase1.GRCh38,MafDb.1Kgenomes.phase1.hs37d5,MafDb.1Kgenomes.phase3.GRCh38,MafDb.1Kgenomes.phase3.hs37d5,MafDb.ExAC.r1.0.GRCh38,MafDb.ExAC.r1.0.hs37d5,MafDb.ExAC.r1.0.nonTCGA.GRCh38,MafDb.ExAC.r1.0.nonTCGA.hs37d5,MafDb.gnomAD.r2.1.GRCh38,MafDb.gnomAD.r2.1.hs37d5,MafDb.gnomAD.r3.0.GRCh38,MafDb.gnomADex.r2.1.GRCh38,MafDb.gnomADex.r2.1.hs37d5,MafDb.TOPMed.freeze5.hg19,MafDb.TOPMed.freeze5.hg38,MafH5.gnomAD.r3.0.GRCh38,methrix,MethylSeekR,MMDiff2,motifbreakR,motifmatchr,msgbsR,phastCons100way.UCSC.hg19,phastCons100way.UCSC.hg38,phastCons7way.UCSC.hg38,,pipeFrame,podkat,PWMEnrich,qsea,QuasR,R453Plus1Toolbox,RareVariantVis,美国广播公司,地区,REMP,Repitools,ribosomeProfilingQC,RNAmodR,scmeth,范围,seqplots,SigsPack,SNPlocs.Hsapiens.dbSNP.20120608,SNPlocs.Hsapiens.dbSNP141.GRCh38,SNPlocs.Hsapiens.dbSNP142.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh38,SNPlocs.Hsapiens.dbSNP149.GRCh38,SNPlocs.Hsapiens.dbSNP150.GRCh38,SNPlocs.Hsapiens.dbSNP151.GRCh38,SparseSignatures,TAPseq,TFBSTools,trena,tRNAscanImport,Ularcirc,VariantAnnotation,VariantFiltering,VariantTools,XtraSNPlocs.Hsapiens.dbSNP141.GRCh38,XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
建议我 Biostrings,biovizBase,chipseq,easyRNASeq,eisaR,GeneRegionScan,GenomeInfoDb,GenomicAlignments,GenomicFeatures,GenomicRanges,genoset,maftools,metaseqR,metaseqR2,海市蜃楼,MutationalPatterns,ORFik,QDNAseq,收回,rtracklayer,SNPlocs.Hsapiens.dbSNP.20101109,waveTiling
我的链接
构建报告

包档案

遵循bob 体育网址 指示在R会话中使用这个包。

源包 BSgenome_1.56.0.tar.gz
Windows二进制 BSgenome_1.56.0.zip
macOS 10.13(高山脉) BSgenome_1.56.0.tgz
源库 git克隆https://git.bioconductor.org/packages/BSgenome
源库(开发人员访问) git克隆git@git.bioconductor.org:包/ BSgenome
包短Url //www.anjoumacpherson.com/packages/BSgenome/
包下载报告 下载数据

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