AnnotationDbi

DOI: 10.18129/B9.bioc.AnnotationDbi    

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

Manipulation of SQLite-based annotations in Bioconductor

Bioconductor version: Development (3.17)

Implements a user-friendly interface for querying SQLite-based annotation data packages.

Author: Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("AnnotationDbi")):

Installation

To install this package, start R (version "4.3") 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")

 

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

Details

biocViews Annotation, GenomeAnnotation, Microarray, Sequencing, Software
Version 1.61.0
In Bioconductor since BioC 2.1 (R-2.6) (15 years)
License Artistic-2.0
Depends R (>= 2.7.0), methods, utils, stats4, BiocGenerics(>= 0.29.2), Biobase(>= 1.17.0), IRanges
Imports DBI, RSQLite, S4Vectors(>= 0.9.25), stats, KEGGREST
LinkingTo
Suggests 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
SystemRequirements
Enhances
URL https://bioconductor.org/packages/AnnotationDbi
BugReports https://github.com/Bioconductor/AnnotationDbi/issues
Depends On Me annotate, AnnotationForge, ASpli, attract, Category, ChromHeatMap, customProDB, deco, 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, crisprseekplus, CrispRVariants, crossmeta, cTRAP, debrowser, derfinder, DeSousa2013, DominoEffect, DOSE, EasyCellType, EDASeq, eegc, EnrichmentBrowser, ensembldb, EpiMix, epimutacions, erma, esATAC, ExpHunterSuite, FRASER, GA4GHshiny, gage, GAPGOM, genefilter, geneplotter, GeneTonic, geneXtendeR, GenomicInteractionNodes, GenVisR, ggbio, GlobalAncova, globaltest, GmicR, GOfuncR, GOpro, GOSemSim, goseq, GOSim, goSTAG, GOstats, goTools, graphite, GSEABase, GSEABenchmarkeR, Gviz, gwascat, ideal, IMAS, InPAS, interactiveDisplay, IRISFGM, isomiRs, IVAS, karyoploteR, KEGGlincs, keggorthology, LRBaseDbi, lumi, mAPKL, MCbiclust, MeSHDbi, meshes, MesKit, MetaboSignal, methylGSA, methylumi, MIGSA, MineICA, MiRaGE, mirIntegrator, miRNAmeConverter, missMethyl, MLP, msigdb, MSnID, multiGSEA, multiMiR, NanoMethViz, NanoStringQCPro, nanotatoR, netOmics, NetSAM, netZooR, NoRCE, ORFik, Organism.dplyr, PADOG, pathview, pcaExplorer, phantasus, phenoTest, proActiv, psichomics, pwOmics, qpgraph, QuasR, rCGH, ReactomePA, REDseq, regutools, ReportingTools, restfulSE, rGREAT, rgsepd, ribosomeProfilingQC, RNAAgeCalc, rrvgo, rTRM, SBGNview, scanMiRApp, scPipe, scRNAseq, scruff, scTensor, SGSeq, signatureSearch, signifinder, simplifyEnrichment, SMITE, SpidermiR, StarBioTrek, SubCellBarCode, TCGAutils, tenXplore, TFutils, tigre, trackViewer, trena, TRESS, tricycle, txcutr, 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, gCrisprTools, GeneRegionScan, GenomicRanges, iSEEu, limma, miRLAB, MutationalPatterns, NetActivity, oligo, ontoProc, OUTRIDER, piano, Pigengene, plotgardener, pRoloc, ProteoDisco, quantiseqr, R3CPET, recount, RforProteomics, RLSeq, sigPathway, sparrow, SummarizedExperiment, systemPipeR, tidybulk, topconfects, weitrix, wiggleplotr
Links To Me
Build Report  

Package Archives

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

Source Package AnnotationDbi_1.61.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/AnnotationDbi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AnnotationDbi
Package Short Url https://bioconductor.org/packages/AnnotationDbi/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: