BSgenome

DOI:10.18129 / B9.bioc.BSgenome

高效表示全基因组及其snp的软件基础设施

Bioconductor版本:发行版(3.16)

所有基于biostrings的基因组数据包共享的基础设施。

作者:Hervé Pagès [aut, cre]， Prisca Chidimma Maduka [ctb](添加'replace'参数到forgeBSgenomeDataPkg())

维护者:Hervé Pagès

安装

要安装这个包，启动R(版本“4.2”)并输入:

如果(!require("BiocManager"， quiet = TRUE)) install.packages("BiocManager")

对于R的旧版本，请参考相应的Bioconductor释放．

文档

要查看系统中安装的此包版本的文档，请启动R并输入:

browseVignettes(“BSgenome”)

PDF	R脚本	利用Biostrings和BSgenome数据包进行高效的基因组搜索
PDF	R脚本	如何伪造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	1.66.2
在Bioconductor	BioC 1.9 (R-2.4)(16.5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(> = 1.25.6),GenomicRanges(> = 1.31.10),Biostrings(> = 2.47.6),rtracklayer(> = 1.39.7)
进口	方法，utils，统计，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.andersvercelli.com/packages/BSgenome
BugReports	https://github.com/Bioconductor/BSgenome/issues
全靠我	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.Hsapiens.UCSC.hs1，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.Hsapiens.UCSC.hs1，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，crisprViz，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，解决，ribosomeProfilingQC，RNAmodR，scmeth，范围，签名者，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，有尖刺的，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
链接到我
构建报告

包档案

遵循2021年欧洲杯比分预测 在R会话中使用此包的说明。

源包	BSgenome_1.66.2.tar.gz
Windows二进制	BSgenome_1.66.2.zip
macOS二进制文件(x86_64)	BSgenome_1.66.2.tgz
macOS二进制文件(arm64)	BSgenome_1.66.1.tgz
源库	git克隆https://git.bioconductor.org/packages/BSgenome
源存储库(开发人员访问)	git克隆git@git.bioconductor.org:packages/BSgenome
生物包浏览器	https://code.bioconductor.org/browse/BSgenome/
包短Url	//www.andersvercelli.com/packages/BSgenome/
软件包下载报告	下载数据
BioC 3.16的旧源包	源存档