AnnotationDbi

This is the development version of AnnotationDbi; for the stable release version, see AnnotationDbi.

Manipulation of SQLite-based annotations in Bioconductor

Installation

To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("AnnotationDbi")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("AnnotationDbi")

1. Introduction To Bioconductor Annotation Packages	PDF	R Script
2. (Deprecated) How to use bimaps from the ".db" annotation packages	PDF	R Script
Reference Manual	PDF
NEWS	Text
Using AnnotationDb objects	Video

Details

biocViews	Annotation, GenomeAnnotation, Microarray, Sequencing, Software
Version	1.67.0
In Bioconductor since	BioC 2.1 (R-2.6) (16.5 years)
License	Artistic-2.0
Depends	R (>= 2.7.0), methods, stats4, BiocGenerics(>= 0.29.2), Biobase(>= 1.17.0), IRanges
Imports	DBI, RSQLite, S4Vectors(>= 0.9.25), stats, KEGGREST
System Requirements
URL	https://bioconductor.org/packages/AnnotationDbi
Bug Reports	https://github.com/Bioconductor/AnnotationDbi/issues

See More

Suggests	utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr
Linking To
Enhances
Depends On Me	annotate, AnnotationForge, ASpli, attract, Category, ChromHeatMap, customProDB, DEXSeq, EGSEA, EpiTxDb, GenomicFeatures, goProfiles, GSReg, Guitar, ipdDb, maPredictDSC, MGFM, miRNAtap, OrganismDbi, pathRender, proBAMr, rnaseqGene, safe, SemDist, tinesath1probe, topGO
Imports Me	adSplit, affycoretools, affylmGUI, AllelicImbalance, annaffy, AnnotationHub, AnnotationHubData, annotatr, artMS, beadarray, bioCancer, BiocSet, biomaRt, BioNAR, BioNet, biovizBase, bumphunter, BUSpaRse, categoryCompare, ccmap, celldex, cellity, chimeraviz, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPseeker, clusterProfiler, CoCiteStats, Cogito, compEpiTools, consensusDE, crisprDesign, CrispRVariants, crossmeta, cTRAP, Damsel, debrowser, derfinder, DeSousa2013, DominoEffect, DOSE, doubletrouble, EasyCellType, EDASeq, EnrichmentBrowser, ensembldb, EpiMix, epimutacions, erma, esATAC, ExpHunterSuite, FRASER, GA4GHshiny, gage, gDNAx, genefilter, geneplotter, GeneTonic, geneXtendeR, GenomicInteractionNodes, GenVisR, ggbio, ggkegg, gINTomics, GlobalAncova, globaltest, GmicR, GOfuncR, GOpro, GOSemSim, goseq, goSTAG, GOstats, goTools, graphite, GSEABase, GSEABenchmarkeR, Gviz, gwascat, ideal, IMAS, InPAS, interactiveDisplay, isomiRs, IVAS, karyoploteR, KEGGlincs, keggorthology, LRBaseDbi, lumi, magpie, mastR, MCbiclust, MeSHDbi, meshes, MesKit, MetaboSignal, methylGSA, methylumi, MineICA, MiRaGE, mirIntegrator, MIRit, miRNAmeConverter, missMethyl, MLP, mosdef, msigdb, MSnID, multiGSEA, multiMiR, NanoMethViz, nanotatoR, netOmics, NetSAM, netZooR, NoRCE, ORFik, Organism.dplyr, OutSplice, PADOG, pathview, pcaExplorer, phantasus, phenoTest, proActiv, psichomics, qpgraph, QuasR, RAIDS, rCGH, ReactomePA, REDseq, regutools, ReportingTools, rGREAT, rgsepd, ribosomeProfilingQC, RNAAgeCalc, rrvgo, rTRM, SBGNview, scanMiRApp, scPipe, scRNAseq, scruff, scTensor, SGSeq, signatureSearch, signifinder, simplifyEnrichment, SMITE, SubCellBarCode, SVMDO, TCGAutils, tenXplore, TFutils, tigre, trackViewer, TRESS, tricycle, txcutr, txdbmaker, tximeta, Ularcirc, UniProt.ws, VariantAnnotation, VariantFiltering, ViSEAGO
Suggests Me	APAlyzer, ASURAT, autonomics, bambu, BiocGenerics, BiocOncoTK, BioPlex, BloodCancerMultiOmics2017, CellTrails, cicero, cola, csaw, curatedAdipoChIP, DAPAR, DEGreport, edgeR, eisaR, enrichplot, esetVis, FELLA, FGNet, fgsea, fishpond, GA4GHclient, gatom, gCrisprTools, GeDi, GeneRegionScan, GenomicPlot, GenomicRanges, gsean, hpar, iNETgrate, iSEEu, limma, miRLAB, MutationalPatterns, NetActivity, oligo, ontoProc, OUTRIDER, pathlinkR, piano, Pigengene, plotgardener, pRoloc, ProteoDisco, quantiseqr, R3CPET, recount, RforProteomics, simona, SingleCellAlleleExperiment, sparrow, spatialHeatmap, SpliceWiz, SummarizedExperiment, systemPipeR, tidybulk, topconfects, weitrix, wiggleplotr
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	AnnotationDbi_1.67.0.tar.gz
Windows Binary	AnnotationDbi_1.67.0.zip
macOS Binary (x86_64)	AnnotationDbi_1.65.2.tgz
macOS Binary (arm64)	AnnotationDbi_1.65.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AnnotationDbi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AnnotationDbi
Bioc Package Browser	https://code.bioconductor.org/browse/AnnotationDbi/
Package Short Url	https://bioconductor.org/packages/AnnotationDbi/
Package Downloads Report	Download Stats