AnnotationDbi

DOI: 10.18129/B9.bioc.AnnotationDbi    

This is the development version of AnnotationDbi; to use it, please install the devel version of Bioconductor.

Manipulation of SQLite-based annotations in Bioconductor

Bioconductor version: Development (3.10)

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 "3.6") and enter:

if (!requireNamespace("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
Text   NEWS
Video   Using AnnotationDb objects

Details

biocViews Annotation, GenomeAnnotation, Microarray, Sequencing, Software
Version 1.47.0
In Bioconductor since BioC 2.1 (R-2.6) (11.5 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)
LinkingTo
Suggests hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me a4Base, a4Preproc, annotate, AnnotationForge, AnnotationFuncs, attract, Category, chimera, ChromHeatMap, customProDB, deco, DEXSeq, EGSEA, eisa, ExpressionView, FEM, GenomicFeatures, GGdata, GOFunction, goProfiles, GSReg, Guitar, ipdDb, maPredictDSC, MGFM, miRNAtap, MLP, OrganismDbi, pathRender, PGSEA, proBAMr, rnaseqGene, RpsiXML, safe, SemDist, tinesath1probe, topGO
Imports Me adSplit, affycoretools, AllelicImbalance, annaffy, AnnotationHub, AnnotationHubData, annotatr, artMS, ASpli, beadarray, biomaRt, BioNet, biovizBase, bumphunter, CancerMutationAnalysis, categoryCompare, ccmap, cellity, chimeraviz, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPseeker, clusterProfiler, CoCiteStats, compEpiTools, consensusDE, crisprseekplus, CrispRVariants, crossmeta, csaw, DAPAR, debrowser, derfinder, DeSousa2013, DominoEffect, DOSE, dSimer, EDASeq, eegc, EnrichmentBrowser, enrichplot, ensembldb, erma, esATAC, ExpressionView, GA4GHshiny, gage, GAPGOM, gCMAP, gCMAPWeb, genefilter, geneplotter, geneXtendeR, GenVisR, GGBase, ggbio, GGtools, GlobalAncova, globaltest, GOfuncR, GOFunction, GOpro, GOSemSim, goseq, GOSim, goSTAG, GOstats, goTools, gpart, gQTLstats, graphite, GSEABase, GSEABenchmarkeR, Gviz, gwascat, HTSanalyzeR, ideal, IMAS, InPAS, interactiveDisplay, iSEE, isomiRs, IVAS, karyoploteR, KEGGlincs, keggorthology, KEGGprofile, LRBaseDbi, lumi, mAPKL, MCbiclust, mdgsa, MeSHDbi, meshes, MetaboSignal, methyAnalysis, methylGSA, methylumi, MIGSA, MineICA, MiRaGE, mirIntegrator, miRNAmeConverter, missMethyl, multiMiR, NanoStringQCPro, nanotatoR, Onassis, ontoProc, ORFik, Organism.dplyr, PADOG, pathview, PathwaySplice, pcaExplorer, pcaGoPromoter, PCpheno, PGA, phantasus, phenoTest, ppiData, psichomics, pwOmics, qpgraph, QuasR, RCAS, rCGH, ReactomePA, REDseq, ReportingTools, restfulSE, rgsepd, rTRM, ScISI, scPipe, scruff, scTensor, SGSeq, singleCellTK, SLGI, SMITE, SpidermiR, StarBioTrek, TCGAutils, tenXplore, tigre, trackViewer, trena, tximeta, UniProt.ws, VariantAnnotation, VariantFiltering
Suggests Me BiocCaseStudies, BiocGenerics, BiocOncoTK, BloodCancerMultiOmics2017, CellTrails, cicero, cola, curatedAdipoChIP, DEGreport, edgeR, esetVis, FELLA, FGNet, fgsea, GA4GHclient, gCrisprTools, geecc, GeneAnswers, GeneRegionScan, GenomicRanges, limma, miRLAB, MmPalateMiRNA, oligo, oligo, OUTRIDER, piano, Pigengene, pRoloc, qcmetrics, R3CPET, recount, RforProteomics, RGalaxy, sigPathway, SummarizedExperiment, TFutils, topconfects, wiggleplotr
Links To Me
Build Report  

Package Archives

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

Source Package AnnotationDbi_1.47.0.tar.gz
Windows Binary AnnotationDbi_1.47.0.zip
Mac OS X 10.11 (El Capitan) AnnotationDbi_1.47.0.tgz
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 http://bioconductor.org/packages/AnnotationDbi/
Package Downloads Report Download Stats

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