BSgenome

DOI:10.18129 / B9.bioc.BSgenome

这是发展BSgenome版本;稳定的发布版本,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:发展(3.16)

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.on。github在gmail.com >

安装

安装这个包,开始R(版本“4.2”)并输入:

如果(!要求(“BiocManager”,悄悄地= TRUE)) install.packages (BiocManager) #以下初始化使用Bioc猛击BiocManager::安装(version =“重击”)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	1.65.2
Bioconductor自	BioC 1.9 (r - 2.4)(16岁)
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(> = 1.25.6),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(> = 0.29.3),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	//www.anjoumacpherson.com/packages/BSgenome
BugReports	https://github.com/Bioconductor/BSgenome/issues
取决于我	注释,bambu,BSgenome.Alyrata.JGI.v1,BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.NCBI.AmelHAv3.1,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.Btaurus.UCSC.bosTau9.masked,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.Cjacchus.UCSC.calJac4,BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1,BSgenome.Creinhardtii.JGI.v5.6,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.Gmax.NCBI.Gmv40,BSgenome.Hsapiens.1000genomes.hs37d5,BSgenome.Hsapiens.NCBI.GRCh38,BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0,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.dbSNP151.major,BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor,BSgenome.Hsapiens.UCSC.hg38.masked,BSgenome.Mdomestica.UCSC.monDom5,BSgenome.Mfascicularis.NCBI.5.0,BSgenome.Mfascicularis.NCBI.6.0,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.mm39,BSgenome.Mmusculus.UCSC.mm8,BSgenome.Mmusculus.UCSC.mm8.masked,BSgenome.Mmusculus.UCSC.mm9,BSgenome.Mmusculus.UCSC.mm9.masked,BSgenome.Osativa.MSU.MSU7,BSgenome.Ppaniscus.UCSC.panPan1,BSgenome.Ppaniscus.UCSC.panPan2,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.Rnorvegicus.UCSC.rn7,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,periodicDNA,REDseq,rGADEM,SNPlocs.Hsapiens.dbSNP144.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh38,SNPlocs.Hsapiens.dbSNP149.GRCh38,SNPlocs.Hsapiens.dbSNP150.GRCh38,SNPlocs.Hsapiens.dbSNP155.GRCh37,SNPlocs.Hsapiens.dbSNP155.GRCh38,VarCon,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.NCBI.AmelHAv3.1,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.Btaurus.UCSC.bosTau9.masked,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.Cjacchus.UCSC.calJac4,BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1,BSgenome.Creinhardtii.JGI.v5.6,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.Gmax.NCBI.Gmv40,BSgenome.Hsapiens.NCBI.GRCh38,BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0,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.Mfascicularis.NCBI.6.0,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.mm39,BSgenome.Mmusculus.UCSC.mm8,BSgenome.Mmusculus.UCSC.mm8.masked,BSgenome.Mmusculus.UCSC.mm9,BSgenome.Mmusculus.UCSC.mm9.masked,BSgenome.Osativa.MSU.MSU7,BSgenome.Ppaniscus.UCSC.panPan1,BSgenome.Ppaniscus.UCSC.panPan2,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.Rnorvegicus.UCSC.rn7,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,chromVAR,circRNAprofiler,cleanUpdTSeq,cliProfiler,crisprBowtie,crisprBwa,crisprDesign,CRISPRseek,crisprseekplus,diffHic,dpeak,enhancerHomologSearch,enrichTF,esATAC,EventPointer,exomePeak2,fitCons.UCSC.hg19,弗雷泽,gcapc,genomation,GenomicDistributionsData,GenVisR,ggbio,gmapR,GreyListChIP,GUIDEseq,Gviz,hiAnnotator,HiCDCPlus,InPAS,IsoformSwitchAnalyzeR,katdetectr,m6Aboost,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.gnomADex.r2.1.GRCh38,MafDb.gnomADex.r2.1.hs37d5,MafDb.TOPMed.freeze5.hg19,MafDb.TOPMed.freeze5.hg38,MafH5.gnomAD.v3.1.1.GRCh38,MafH5.gnomAD.v3.1.2.GRCh38,methrix,MethylSeekR,MMDiff2,蒙娜丽莎,Motif2Site,motifbreakR,motifmatchr,msgbsR,multicrispr,MungeSumstats,musicatk,MutationalPatterns,NxtIRFcore,ORFik,phastCons100way.UCSC.hg19,phastCons100way.UCSC.hg38,phastCons7way.UCSC.hg38,平,pipeFrame,podkat,qsea,QuasR,R453Plus1Toolbox,RareVariantVis,美国广播公司,地区,REMP,Repitools,ribosomeProfilingQC,RNAmodR,scmeth,范围,SigsPack,SingleMoleculeFootprinting,SNPlocs.Hsapiens.dbSNP144.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh38,SNPlocs.Hsapiens.dbSNP149.GRCh38,SNPlocs.Hsapiens.dbSNP150.GRCh38,SNPlocs.Hsapiens.dbSNP155.GRCh37,SNPlocs.Hsapiens.dbSNP155.GRCh38,SparseSignatures,spatzie,的,SpliceWiz,TAPseq,TFBSTools,trena,tRNAscanImport,Ularcirc,UMI4Cats,VariantAnnotation,VariantFiltering,VariantTools,XNAString,XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
建议我	Biostrings,biovizBase,ChIPpeakAnno,chipseq,easyRNASeq,eisaR,factR,GeneRegionScan,GenomeInfoDb,GenomicAlignments,GenomicFeatures,GenomicRanges,maftools,metaseqR2,海市蜃楼,plotgardener,ProteoDisco,PWMEnrich,QDNAseq,收回,RiboCrypt,rtracklayer,sitadela
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_1.65.2.tar.gz
Windows二进制	BSgenome_1.65.2.zip
macOS 10.13(高山脉)	BSgenome_1.65.2.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