annotate

Annotation for microarrays


Bioconductor version: Release (3.19)

Using R enviroments for annotation.

Author: R. Gentleman

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

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

Installation

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


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

BiocManager::install("annotate")

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("annotate")
Annotation Overview PDF R Script
Basic GO Usage PDF R Script
HowTo: Build and use chromosomal information HTML R Script
HowTo: Get HTML Output PDF R Script
HOWTO: Use the online query tools PDF R Script
Using Affymetrix Probe Level Data PDF R Script
Using Bioconductor's Annotation Libraries HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, GO, Pathways, Software
Version 1.82.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19.5 years)
License Artistic-2.0
Depends R (>= 2.10), AnnotationDbi(>= 1.27.5), XML
Imports Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics(>= 0.13.8), httr
System Requirements
URL
See More
Suggests hgu95av2.db, genefilter, Biostrings(>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr
Linking To
Enhances
Depends On Me ChromHeatMap, GSEABase, MLInterfaces, MineICA, PREDA, SemDist, geneplotter, idiogram, phenoTest, sampleClassifier, Neve2006, PREDAsampledata
Imports Me CAFE, CNEr, Category, DrugVsDisease, GOstats, GlobalAncova, MGFR, SGCP, UMI4Cats, categoryCompare, codelink, debrowser, genefilter, globaltest, lumi, methylumi, phenoTest, qpgraph, tigre, easyDifferentialGeneCoexpression, geneExpressionFromGEO, GOxploreR
Suggests Me BiocGenerics, GSAR, GSEAlm, GenomicRanges, MLP, PhosR, RnBeads, SummarizedExperiment, hmdbQuery, metagenomeSeq, pageRank, pcxn, siggenes, systemPipeR, adme16cod.db, ag.db, ath1121501.db, bovine.db, canine.db, canine2.db, celegans.db, chicken.db, clariomdhumanprobeset.db, clariomdhumantranscriptcluster.db, clariomshumanhttranscriptcluster.db, clariomshumantranscriptcluster.db, clariomsmousehttranscriptcluster.db, clariomsmousetranscriptcluster.db, clariomsrathttranscriptcluster.db, clariomsrattranscriptcluster.db, drosgenome1.db, drosophila2.db, ecoli2.db, GGHumanMethCancerPanelv1.db, h10kcod.db, h20kcod.db, hcg110.db, hgfocus.db, hgu133a.db, hgu133a2.db, hgu133b.db, hgu133plus2.db, hgu219.db, hgu95a.db, hgu95av2.db, hgu95b.db, hgu95c.db, hgu95d.db, hgu95e.db, hguatlas13k.db, hgubeta7.db, hguDKFZ31.db, hgug4100a.db, hgug4101a.db, hgug4110b.db, hgug4111a.db, hgug4112a.db, hgug4845a.db, hguqiagenv3.db, hi16cod.db, hs25kresogen.db, Hs6UG171.db, HsAgilentDesign026652.db, hta20probeset.db, hta20transcriptcluster.db, hthgu133a.db, hthgu133b.db, hthgu133plusa.db, hthgu133plusb.db, hthgu133pluspm.db, htmg430a.db, htmg430b.db, htmg430pm.db, htrat230pm.db, htratfocus.db, hu35ksuba.db, hu35ksubb.db, hu35ksubc.db, hu35ksubd.db, hu6800.db, huex10stprobeset.db, huex10sttranscriptcluster.db, hugene10stprobeset.db, hugene10sttranscriptcluster.db, hugene11stprobeset.db, hugene11sttranscriptcluster.db, hugene20stprobeset.db, hugene20sttranscriptcluster.db, hugene21stprobeset.db, hugene21sttranscriptcluster.db, HuO22.db, hwgcod.db, IlluminaHumanMethylation27k.db, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv2BeadID.db, illuminaHumanv3.db, illuminaHumanv4.db, illuminaHumanWGDASLv3.db, illuminaHumanWGDASLv4.db, illuminaMousev1.db, illuminaMousev1p1.db, illuminaMousev2.db, illuminaRatv1.db, indac.db, JazaeriMetaData.db, LAPOINTE.db, lumiHumanAll.db, lumiMouseAll.db, lumiRatAll.db, m10kcod.db, m20kcod.db, mgu74a.db, mgu74av2.db, mgu74b.db, mgu74bv2.db, mgu74c.db, mgu74cv2.db, mguatlas5k.db, mgug4104a.db, mgug4120a.db, mgug4121a.db, mgug4122a.db, mi16cod.db, miRBaseVersions.db, mm24kresogen.db, MmAgilentDesign026655.db, moe430a.db, moe430b.db, moex10stprobeset.db, moex10sttranscriptcluster.db, mogene10stprobeset.db, mogene10sttranscriptcluster.db, mogene11stprobeset.db, mogene11sttranscriptcluster.db, mogene20stprobeset.db, mogene20sttranscriptcluster.db, mogene21stprobeset.db, mogene21sttranscriptcluster.db, mouse4302.db, mouse430a2.db, mpedbarray.db, mta10probeset.db, mta10transcriptcluster.db, mu11ksuba.db, mu11ksubb.db, Mu15v1.db, mu19ksuba.db, mu19ksubb.db, mu19ksubc.db, Mu22v3.db, mwgcod.db, Norway981.db, nugohs1a520180.db, nugomm1a520177.db, OperonHumanV3.db, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, Orthology.eg.db, PartheenMetaData.db, pedbarrayv10.db, pedbarrayv9.db, POCRCannotation.db, porcine.db, r10kcod.db, rae230a.db, rae230b.db, raex10stprobeset.db, raex10sttranscriptcluster.db, ragene10stprobeset.db, ragene10sttranscriptcluster.db, ragene11stprobeset.db, ragene11sttranscriptcluster.db, ragene20stprobeset.db, ragene20sttranscriptcluster.db, ragene21stprobeset.db, ragene21sttranscriptcluster.db, rat2302.db, rgu34a.db, rgu34b.db, rgu34c.db, rguatlas4k.db, rgug4105a.db, rgug4130a.db, rgug4131a.db, ri16cod.db, RnAgilentDesign028282.db, rnu34.db, Roberts2005Annotation.db, rta10probeset.db, rta10transcriptcluster.db, rtu34.db, rwgcod.db, SHDZ.db, SomaScan.db, u133x3p.db, xlaevis.db, yeast2.db, ygs98.db, zebrafish.db, clValid, limorhyde, maGUI, MOSS
Links To Me
Build Report Build Report

Package Archives

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

Source Package annotate_1.82.0.tar.gz
Windows Binary (x86_64) annotate_1.82.0.zip
macOS Binary (x86_64) annotate_1.82.0.tgz
macOS Binary (arm64) annotate_1.82.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/annotate
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/annotate
Bioc Package Browser https://code.bioconductor.org/browse/annotate/
Package Short Url https://bioconductor.org/packages/annotate/
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