AnnotationDbi

DOI:10.18129 / B9.bioc.AnnotationDbi

在Bioconductor中操作基于sqlite的注释

Bioconductor版本:Release (3.15)

实现一个用户友好的界面,用于查询基于sqlite的注释数据包。

作者:Hervé Pagès, Marc Carlson, Seth Falcon,李年华

维护者:Bioconductor Package维护者< Maintainer at Bioconductor .org>

引文(从R内,输入引用(“AnnotationDbi”)):

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(“AnnotationDbi”)

PDF R脚本 1.简介Bioconductor注释包
PDF R脚本 2.(已弃用)如何使用".db"注释包中的bimaps
PDF 参考手册
文本 新闻
视频 使用AnnotationDb对象

细节

biocViews 注释GenomeAnnotation微阵列测序软件
版本 1.58.0
在Bioconductor BioC 2.1 (R-2.6)(15年)
许可证 艺术- 2.0
取决于 R(>= 2.7.0),方法,utils, stats4,BiocGenerics(> = 0.29.2),Biobase(> = 1.17.0),IRanges
进口 DBIRSQLiteS4Vectors(>= 0.9.25), stats,KEGGREST
链接
建议 hgu95av2.dbGO.dborg.Sc.sgd.dborg.At.tair.dbRUnitTxDb.Hsapiens.UCSC.hg19.knownGeneorg.Hs.eg.dbreactome.dbAnnotationForgeEnsDb.Hsapiens.v75BiocStyleknitr
SystemRequirements
增强了
URL //www.anjoumacpherson.com/packages/AnnotationDbi
BugReports https://github.com/Bioconductor/AnnotationDbi/issues
全靠我 adme16cod.dbag.dbagprobe注释AnnotationForgeanopheles.db0arabidopsis.db0ASpliath1121501.dbath1121501probe吸引barley1probebovine.dbbovine.db0bovineprobebsubtilisprobecanine.dbcanine.db0canine2.dbcanine2probecanineprobe类别celegans.dbcelegansprobechicken.dbchicken.db0chickenprobechimp.db0ChromHeatMapcitrusprobeclariomdhumanprobeset.dbclariomdhumantranscriptcluster.dbclariomshumanhttranscriptcluster.dbclariomshumantranscriptcluster.dbclariomsmousehttranscriptcluster.dbclariomsmousetranscriptcluster.dbclariomsrathttranscriptcluster.dbclariomsrattranscriptcluster.dbcottonprobecustomProDB德科DEXSeqDO.dbdrosgenome1.dbdrosgenome1probedrosophila2.dbdrosophila2probeecoli2.dbecoli2probeecoliasv2probeecoliK12.db0ecoliprobeecoliSakai.db0EGSEAEpiTxDbfly.db0GenomicFeaturesGGHumanMethCancerPanelv1.dbGO.dbgoProfilesGSReg吉他h10kcod.dbh20kcod.dbhcg110.dbhcg110probehgfocus.dbhgfocusprobehgu133a.dbhgu133a2.dbhgu133a2probehgu133aprobehgu133atagprobehgu133b.dbhgu133bprobehgu133plus2.dbhgu133plus2probehgu219.dbhgu219probehgu95a.dbhgu95aprobehgu95av2.dbhgu95av2probehgu95b.dbhgu95bprobehgu95c.dbhgu95cprobehgu95d.dbhgu95dprobehgu95e.dbhgu95eprobehguatlas13k.dbhgubeta7.dbhguDKFZ31.dbhgug4100a.dbhgug4101a.dbhgug4110b.dbhgug4111a.dbhgug4112a.dbhgug4845a.dbhguqiagenv3.dbhi16cod.dbHomo.sapienshs25kresogen.dbHs6UG171.dbHsAgilentDesign026652.dbhta20probeset.dbhta20transcriptcluster.dbhthgu133a.dbhthgu133aprobehthgu133b.dbhthgu133bprobehthgu133plusa.dbhthgu133plusb.dbhthgu133pluspm.dbhthgu133pluspmprobehtmg430a.dbhtmg430aprobehtmg430b.dbhtmg430bprobehtmg430pm.dbhtmg430pmprobehtrat230pm.dbhtrat230pmprobehtratfocus.dbhtratfocusprobehu35ksuba.dbhu35ksubaprobehu35ksubb.dbhu35ksubbprobehu35ksubc.dbhu35ksubcprobehu35ksubd.dbhu35ksubdprobehu6800.dbhu6800probehuex10stprobeset.dbhuex10sttranscriptcluster.dbHuExExonProbesetLocationHuExExonProbesetLocationHg18HuExExonProbesetLocationHg19hugene10stprobeset.dbhugene10sttranscriptcluster.dbhugene10stv1probehugene11stprobeset.dbhugene11sttranscriptcluster.dbhugene20stprobeset.dbhugene20sttranscriptcluster.dbhugene21stprobeset.dbhugene21sttranscriptcluster.dbhuman.db0HuO22.dbhwgcod.dbIlluminaHumanMethylation27k.dbIlluminaHumanMethylation450kprobeilluminaHumanv1.dbilluminaHumanv2.dbilluminaHumanv2BeadID.dbilluminaHumanv3.dbilluminaHumanv4.dbilluminaHumanWGDASLv3.dbilluminaHumanWGDASLv4.dbilluminaMousev1.dbilluminaMousev1p1.dbilluminaMousev2.dbilluminaRatv1.dbindac.dbipdDbJazaeriMetaData.dbLAPOINTE.dblumiHumanAll.dblumiHumanIDMappinglumiMouseAll.dblumiMouseIDMappinglumiRatAll.dblumiRatIDMappingm10kcod.dbm20kcod.dbmaizeprobemalaria.db0maPredictDSCmedicagoprobeMGFMmgu74a.dbmgu74aprobemgu74av2.dbmgu74av2probemgu74b.dbmgu74bprobemgu74bv2.dbmgu74bv2probemgu74c.dbmgu74cprobemgu74cv2.dbmgu74cv2probemguatlas5k.dbmgug4104a.dbmgug4120a.dbmgug4121a.dbmgug4122a.dbmi16cod.dbmirbase.dbmirna10probemiRNAtapmm24kresogen.dbMmAgilentDesign026655.dbmoe430a.dbmoe430aprobemoe430b.dbmoe430bprobemoex10stprobeset.dbmoex10sttranscriptcluster.dbMoExExonProbesetLocationmogene10stprobeset.dbmogene10sttranscriptcluster.dbmogene10stv1probemogene11stprobeset.dbmogene11sttranscriptcluster.dbmogene20stprobeset.dbmogene20sttranscriptcluster.dbmogene21stprobeset.dbmogene21sttranscriptcluster.dbmouse.db0mouse4302.dbmouse4302probemouse430a2.dbmouse430a2probempedbarray.dbmta10probeset.dbmta10transcriptcluster.dbmu11ksuba.dbmu11ksubaprobemu11ksubb.dbmu11ksubbprobeMu15v1.dbmu19ksuba.dbmu19ksubb.dbmu19ksubc.dbMu22v3.dbMus.musculusmwgcod.dbNorway981.dbnugohs1a520180.dbnugohs1a520180probenugomm1a520177.dbnugomm1a520177probeOperonHumanV3.dborg.Ag.eg.dborg.At.tair.dborg.Bt.eg.dborg.Ce.eg.dborg.Cf.eg.dborg.Dm.eg.dborg.Dr.eg.dborg.EcK12.eg.dborg.EcSakai.eg.dborg.Gg.eg.dborg.Hs.eg.dborg.Mm.eg.dborg.Mmu.eg.dborg.Mxanthus.dborg.Pt.eg.dborg.Rn.eg.dborg.Sc.sgd.dborg.Ss.eg.dborg.Xl.eg.dbOrganismDbiOrthology.eg.dbpaeg1aprobePANTHER.dbPartheenMetaData.dbpathRenderpedbarrayv10.dbpedbarrayv9.dbPFAM.dbpig.db0plasmodiumanophelesprobePOCRCannotation.dbpoplarprobeporcine.dbporcineprobeprimeviewprobeproBAMrr10kcod.dbrae230a.dbrae230aproberae230b.dbrae230bproberaex10stprobeset.dbraex10sttranscriptcluster.dbRaExExonProbesetLocationragene10stprobeset.dbragene10sttranscriptcluster.dbragene10stv1proberagene11stprobeset.dbragene11sttranscriptcluster.dbragene20stprobeset.dbragene20sttranscriptcluster.dbragene21stprobeset.dbragene21sttranscriptcluster.dbrat.db0rat2302.dbrat2302proberattoxfxprobeRattus.norvegicusreactome.dbrgu34a.dbrgu34aprobergu34b.dbrgu34bprobergu34c.dbrgu34cproberguatlas4k.dbrgug4105a.dbrgug4130a.dbrgug4131a.dbrhesus.db0rhesusproberi16cod.dbriceprobeRnAgilentDesign028282.dbrnaseqGenernu34.dbrnu34probeRoberts2005Annotation.dbrta10probeset.dbrta10transcriptcluster.dbrtu34.dbrtu34proberwgcod.db安全saureusprobeSemDistSHDZ.dbsoybeanprobesugarcaneprobetargetscan.Hs.eg.dbtargetscan.Mm.eg.dbtest3probetinesath1probetomatoprobetopGOu133x3p.dbu133x3pprobevitisviniferaprobewheatprobeworm.db0xenopus.db0xenopuslaevisprobexlaevis.dbxlaevis2probextropicalisprobeyeast.db0yeast2.dbyeast2probeygs98.dbygs98probezebrafish.dbzebrafish.db0zebrafishprobe
进口我 adme16cod.dbadSplitaffycoretoolsaffylmGUIag.dbagcdfAllelicImbalanceannaffyAnnotationHubAnnotationHubDataannotatrartMSath1121501.dbath1121501cdfbarley1cdfbeadarraybioCancerBiocSetbiomaRt生命网络biovizBasebovine.dbbovinecdfbsubtiliscdfbumphunterBUSpaRsecanine.dbcanine2.dbcanine2cdfcaninecdfcategoryCompareccmapcelegans.dbceleganscdfcelldexcellitychicken.dbchickencdfchimeravizchipenrichchipenrich.dataChIPpeakAnnoChIPseekercitruscdfclariomdhumanprobeset.dbclariomdhumantranscriptcluster.dbclariomshumanhttranscriptcluster.dbclariomshumantranscriptcluster.dbclariomsmousehttranscriptcluster.dbclariomsmousetranscriptcluster.dbclariomsrathttranscriptcluster.dbclariomsrattranscriptcluster.dbclusterProfilerCoCiteStats我思compEpiToolsconclusconsensusDEcottoncdfcrisprseekplusCrispRVariantscrossmetacTRAPcyp450cdfdebrowserderfinderDeSousa2013DO.dbDominoEffect剂量drosgenome1.dbdrosgenome1cdfdrosophila2.dbdrosophila2cdfecoli2.dbecoli2cdfecoliasv2cdfecolicdfEDASeqeegcEnrichmentBrowserensembldbermaesATACExpHunterSuiteFDb.FANTOM4.promoters.hg19FDb.InfiniumMethylation.hg18FDb.InfiniumMethylation.hg19FDb.UCSC.snp135common.hg19FDb.UCSC.snp137common.hg19FDb.UCSC.tRNAs弗雷泽GA4GHshinyGAPGOMgenefiltergeneplotterGeneTonicgeneXtendeRGenomicInteractionNodesGenomicStateGenVisRggbioGGHumanMethCancerPanelv1.dbGlobalAncovaglobaltestGmicRGOfuncR还装有GOSemSimgoseqGOSimgoSTAGGOstatsgoToolsgp53cdfgpart软件石墨GSEABaseGSEABenchmarkeRGvizgwascath10kcod.dbh20kcod.dbhcg110.dbhcg110cdfhgfocus.dbhgfocuscdfhgu133a.dbhgu133a2.dbhgu133a2cdfhgu133acdfhgu133atagcdfhgu133b.dbhgu133bcdfhgu133plus2.dbhgu133plus2cdfhgu219.dbhgu219cdfhgu95a.dbhgu95acdfhgu95av2.dbhgu95av2cdfhgu95b.dbhgu95bcdfhgu95c.dbhgu95ccdfhgu95d.dbhgu95dcdfhgu95e.dbhgu95ecdfhguatlas13k.dbhgubeta7.dbhguDKFZ31.dbhgug4100a.dbhgug4101a.dbhgug4110b.dbhgug4111a.dbhgug4112a.dbhgug4845a.dbhguqiagenv3.dbhi16cod.dbhivprtplus2cdfHomo.sapienshs25kresogen.dbHs6UG171.dbHsAgilentDesign026652.dbHspechspeccdfhta20probeset.dbhta20transcriptcluster.dbhthgu133a.dbhthgu133acdfhthgu133b.dbhthgu133bcdfhthgu133plusa.dbhthgu133plusb.dbhthgu133pluspm.dbhthgu133pluspmcdfhtmg430a.dbhtmg430acdfhtmg430b.dbhtmg430bcdfhtmg430pm.dbhtmg430pmcdfhtrat230pm.dbhtrat230pmcdfhtratfocus.dbhtratfocuscdfhu35ksuba.dbhu35ksubacdfhu35ksubb.dbhu35ksubbcdfhu35ksubc.dbhu35ksubccdfhu35ksubd.dbhu35ksubdcdfhu6800.dbhu6800cdfhu6800subacdfhu6800subbcdfhu6800subccdfhu6800subdcdfhuex10stprobeset.dbhuex10sttranscriptcluster.dbhugene10stprobeset.dbhugene10sttranscriptcluster.dbhugene10stv1cdfhugene11stprobeset.dbhugene11sttranscriptcluster.dbhugene20stprobeset.dbhugene20sttranscriptcluster.dbhugene21stprobeset.dbhugene21sttranscriptcluster.dbHuO22.dbhwgcod.db理想的IlluminaHumanMethylation27k.dbilluminaHumanv1.dbilluminaHumanv2.dbilluminaHumanv2BeadID.dbilluminaHumanv3.dbilluminaHumanv4.dbilluminaHumanWGDASLv3.dbilluminaHumanWGDASLv4.dbilluminaMousev1.dbilluminaMousev1p1.dbilluminaMousev2.dbilluminaRatv1.dbimaindac.dbInPASinteractiveDisplayIRISFGMisomiRsivaJazaeriMetaData.dbkaryoploteRKEGGlincskeggorthologyLAPOINTE.dbLRBaseDbi光民lumiHumanAll.dblumiHumanIDMappinglumiMouseAll.dblumiMouseIDMappinglumiRatAll.dblumiRatIDMappingm10kcod.dbm20kcod.dbmaizecdfmAPKLMCbiclustmedicagocdfMeSHDbi网格MesKitMetaboSignalmethylGSAmethylumimgu74a.dbmgu74acdfmgu74av2.dbmgu74av2cdfmgu74b.dbmgu74bcdfmgu74bv2.dbmgu74bv2cdfmgu74c.dbmgu74ccdfmgu74cv2.dbmgu74cv2cdfmguatlas5k.dbmgug4104a.dbmgug4120a.dbmgug4121a.dbmgug4122a.dbmi16cod.dbMIGSAMineICA海市蜃楼mirbase.dbmiRBaseVersions.dbmirIntegratormirna102xgaincdfmirna10cdfmirna20cdfmiRNAmeConvertermiRNAtap.dbmissMethyl中长期规划mm24kresogen.dbMmAgilentDesign026655.dbmoe430a.dbmoe430acdfmoe430b.dbmoe430bcdfmoex10stprobeset.dbmoex10sttranscriptcluster.dbmogene10stprobeset.dbmogene10sttranscriptcluster.dbmogene10stv1cdfmogene11stprobeset.dbmogene11sttranscriptcluster.dbmogene20stprobeset.dbmogene20sttranscriptcluster.dbmogene21stprobeset.dbmogene21sttranscriptcluster.dbmouse4302.dbmouse4302cdfmouse430a2.dbmouse430a2cdfmpedbarray.dbmsigdbMSnIDmta10probeset.dbmta10transcriptcluster.dbmu11ksuba.dbmu11ksubacdfmu11ksubb.dbmu11ksubbcdfMu15v1.dbmu19ksuba.dbmu19ksubacdfmu19ksubb.dbmu19ksubbcdfmu19ksubc.dbmu19ksubccdfMu22v3.dbmu6500subacdfmu6500subbcdfmu6500subccdfmu6500subdcdfmultiGSEAmultiMiRMus.musculusmwgcod.dbNanoMethVizNanoStringQCPronanotatoRnetOmicsNetSAMnetZooRNoRCENorway981.dbnugohs1a520180.dbnugohs1a520180cdfnugomm1a520177.dbnugomm1a520177cdf奥纳西斯ontoProcOperonHumanV3.dbORFikOrganism.dplyrPADOGpaeg1acdfPartheenMetaData.dbpathviewpcaExplorerpedbarrayv10.dbpedbarrayv9.dbphantasusphenoTestplasmodiumanophelescdfPOCRCannotation.dbPolyPhen.Hsapiens.dbSNP131poplarcdfporcine.dbporcinecdfppiDataprimeviewcdf高伦雅芙psichomicspwOmicsqpgraphQuasRr10kcod.dbrae230a.dbrae230acdfrae230b.dbrae230bcdfraex10stprobeset.dbraex10sttranscriptcluster.dbragene10stprobeset.dbragene10sttranscriptcluster.dbragene10stv1cdfragene11stprobeset.dbragene11sttranscriptcluster.dbragene20stprobeset.dbragene20sttranscriptcluster.dbragene21stprobeset.dbragene21sttranscriptcluster.dbrat2302.dbrat2302cdfrattoxfxcdfRattus.norvegicusrCGHreactome.dbReactomePAREDseqregutoolsReportingToolsrestfulSErgsepdrgu34a.dbrgu34acdfrgu34b.dbrgu34bcdfrgu34c.dbrgu34ccdfrguatlas4k.dbrgug4105a.dbrgug4130a.dbrgug4131a.dbrhesuscdfri16cod.dbribosomeProfilingQCricecdfRmiR.Hs.miRNARmiR.hsaRNAAgeCalcRnAgilentDesign028282.dbrnu34.dbrnu34cdfRoberts2005Annotation.dbRpsiXMLrrvgorta10probeset.dbrta10transcriptcluster.dbrTRMrtu34.dbrtu34cdfrwgcod.dbsaureuscdfSBGNviewscanMiRAppScISIscPipescRNAseq颈背scTensorSGSeqSHDZ.dbSIFT.Hsapiens.dbSNP132SIFT.Hsapiens.dbSNP137signatureSearchsimplifyEnrichmentSLGI击杀soybeancdfSpidermiRStarBioTrekSubCellBarCodesugarcanecdftargetscan.Hs.eg.dbtargetscan.Mm.eg.dbTCGAutilstenXploretest1cdftest2cdftest3cdfTFutilstigretomatocdftrackViewertrena一绺头发三轮车txcutrTxDb.Athaliana.BioMart.plantsmart22TxDb.Athaliana.BioMart.plantsmart25TxDb.Athaliana.BioMart.plantsmart28TxDb.Athaliana.BioMart.plantsmart51TxDb.Btaurus.UCSC.bosTau8.refGeneTxDb.Btaurus.UCSC.bosTau9.refGeneTxDb.Celegans.UCSC.ce11.ensGeneTxDb.Celegans.UCSC.ce11.refGeneTxDb.Celegans.UCSC.ce6.ensGeneTxDb.Cfamiliaris.UCSC.canFam3.refGeneTxDb.Cfamiliaris.UCSC.canFam4.refGeneTxDb.Cfamiliaris.UCSC.canFam5.refGeneTxDb.Dmelanogaster.UCSC.dm3.ensGeneTxDb.Dmelanogaster.UCSC.dm6.ensGeneTxDb.Drerio.UCSC.danRer10.refGeneTxDb.Drerio.UCSC.danRer11.refGeneTxDb.Ggallus.UCSC.galGal4.refGeneTxDb.Ggallus.UCSC.galGal5.refGeneTxDb.Ggallus.UCSC.galGal6.refGeneTxDb.Hsapiens.BioMart.igisTxDb.Hsapiens.UCSC.hg18.knownGeneTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg19.lincRNAsTranscriptsTxDb.Hsapiens.UCSC.hg38.knownGeneTxDb.Hsapiens.UCSC.hg38.refGeneTxDb.Mmulatta.UCSC.rheMac10.refGeneTxDb.Mmulatta.UCSC.rheMac3.refGeneTxDb.Mmulatta.UCSC.rheMac8.refGeneTxDb.Mmusculus.UCSC.mm10.ensGeneTxDb.Mmusculus.UCSC.mm10.knownGeneTxDb.Mmusculus.UCSC.mm39.refGeneTxDb.Mmusculus.UCSC.mm9.knownGeneTxDb.Ptroglodytes.UCSC.panTro4.refGeneTxDb.Ptroglodytes.UCSC.panTro5.refGeneTxDb.Ptroglodytes.UCSC.panTro6.refGeneTxDb.Rnorvegicus.BioMart.igisTxDb.Rnorvegicus.UCSC.rn4.ensGeneTxDb.Rnorvegicus.UCSC.rn5.refGeneTxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeqTxDb.Rnorvegicus.UCSC.rn6.refGeneTxDb.Rnorvegicus.UCSC.rn7.refGeneTxDb.Scerevisiae.UCSC.sacCer2.sgdGeneTxDb.Scerevisiae.UCSC.sacCer3.sgdGeneTxDb.Sscrofa.UCSC.susScr11.refGeneTxDb.Sscrofa.UCSC.susScr3.refGenetximetau133aaofav2cdfu133x3p.dbu133x3pcdfUlarcircUniProt.wsVariantAnnotationVariantFilteringViSEAGOvitisviniferacdfwheatcdfxenopuslaeviscdfxlaevis.dbxlaevis2cdfxtropicaliscdfye6100subacdfye6100subbcdfye6100subccdfye6100subdcdfyeast2.dbyeast2cdfygs98.dbygs98cdfzebrafish.dbzebrafishcdf
建议我 APAlyzerASURAT自治bambuBiocGenericsBiocOncoTKBioPlexBloodCancerMultiOmics2017CellTrails西塞罗可乐csawcuratedAdipoChIPDAPARDEGreport刨边机eisaRenrichplotepimutacionsesetVis小伙子FGNetfgsea鱼池GA4GHclientgCrisprToolsGeneRegionScanGenomicRangesiSEEulimmamiRLABMutationalPatterns益生元先驱者钢琴PigengeneplotgardenerpRolocProteoDiscoquantiseqrR3CPET重新计票RforProteomicsRLSeqsigPathway麻雀SummarizedExperimentsystemPipeRtidybulktopconfectsweitrixwiggleplotr
链接到我
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源包 AnnotationDbi_1.58.0.tar.gz
Windows二进制 AnnotationDbi_1.58.0.zip
macOS 10.13 (High Sierra) AnnotationDbi_1.58.0.tgz
源库 git克隆https://git.bioconductor.org/packages/AnnotationDbi
源存储库(开发人员访问) git克隆git@git.bioconductor.org:packages/AnnotationDbi
包短Url //www.anjoumacpherson.com/packages/AnnotationDbi/
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