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>

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