Package: annotate 1.89.0

Bioconductor Package Maintainer

annotate: Annotation for microarrays

Using R enviroments for annotation.

Authors:R. Gentleman

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annotate.pdf |annotate.html✨
annotate/json (API)
NEWS

# Install 'annotate' in R:

install.packages('annotate', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

hgByChroms - A dataset to show the human genome base pair locations per chromosome.
hgCLengths - A dataset which contains the lengths (in base pairs) of the human chromosomes.
hgu95AProbLocs - ChromLocation instance hgu95AProbLocs, an example of a chromLocation object
hgu95Achroloc - Annotation data for the Affymetrix HGU95A GeneChip
hgu95Achrom - Annotation data for the Affymetrix HGU95A GeneChip
hgu95All - Annotation data for the Affymetrix HGU95A GeneChip
hgu95Asym - Annotation data for the Affymetrix HGU95A GeneChip

On BioConductor:annotate-1.89.0(bioc 3.23)annotate-1.88.0(bioc 3.22)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

annotation pathways go

11.60 score 231 packages 784 scripts 35k downloads 36 mentions 123 exports 38 dependencies

Last updated from:a7eff2c2f2. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Total time
bioc-checks	WARNING	244
linux-devel-x86_64	NOTE	343
source / vignettes	OK	349
linux-release-x86_64	NOTE	350
macos-release-arm64	NOTE	223
macos-oldrel-arm64	NOTE	239
windows-devel	NOTE	615
windows-release	NOTE	540
windows-oldrel	NOTE	595
wasm-release	OK	190

Exports:.buildAnnotateOpts .efetch .getIdTag .getNcbiURL .handleXML .transformAccession abstText ACC2homology accessionToUID ACCNUMStats allValidKeys annPkgName aqListGOIDs articleTitle authors blastSequences buildChromLocation buildPubMedAbst checkArgs chrCats chromInfo chromLengths chromLocs chromNames clearRepository compatibleVersions createLLChrCats createMAPIncMat dataSource Definition dropECode entrezGeneByID entrezGeneQuery fileName filterGOByOntology findChr4LL findNeighbors genbank geneSymbols getAnnMap getBoundary getEG getEvidence getGI getGO getGOChildren getGOdesc getGOOntology getGOParents getGOTerm getGPLNames getOntology getOrgNameNCode getPMID getPMInfo getQueryLink getRepositories getSAGEFileInfo getSAGEGPL getSEQ getSYMBOL getUniqAnnItem getValidChr GO2heatmap GOID GOmnplot hasGOannote HGID2homology homoACC homoData homoHGID homoLL homoOrg homoPS homoType homoURL htmlpage initialize isValidKey journal KEGG2heatmap KEGGmnplot LL2homology lookUp mainPage makeAnchor mapOrgs nChrom Ontology organism pageText pageTitle pm.abstGrep pm.getabst pm.titles pmAbst2HTML pmid pmid2MIAME PMIDAmat pmidQuery probesToChrom pubDate pubmed pubMedAbst PWAmat readGEOAnn readIDNAcc readUrl Secondary serializeDataPkgEnvs serializeEnv setRepository show sidePage Synonym Term toFile topPage UniGeneQuery updateSymbolsToValidKeys usedChromGenes weightByConfi whatACC

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap generics glue httr IRanges jsonlite KEGGREST lifecycle memoise mime openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors Seqinfo sys vctrs XML xtable XVector

Annotation Overview

Rendered fromannotate.Rnwusingutils::Sweaveon Nov 23 2025.

Last update: 2013-10-25
Started: 2013-10-25

Basic GO Usage

Rendered fromGOusage.Rnwusingutils::Sweaveon Nov 23 2025.

Last update: 2014-04-12
Started: 2013-10-25

HowTo: Build and use chromosomal information

Jeff Gentry, Kritika Verma

Rendered fromchromLOC.Rmdusingknitr::rmarkdownon Nov 23 2025.

Last update: 2024-01-09
Started: 2024-01-09

HowTo: Get HTML Output

Rendered fromprettyOutput.Rnwusingutils::Sweaveon Nov 23 2025.

Last update: 2013-10-25
Started: 2013-10-25

HOWTO: Use the online query tools

Rendered fromquery.Rnwusingutils::Sweaveon Nov 23 2025.

Last update: 2018-03-20
Started: 2013-10-25

Using Affymetrix Probe Level Data

Rendered fromuseProbeInfo.Rnwusingutils::Sweaveon Nov 23 2025.

Last update: 2013-10-25
Started: 2013-10-25

Using Bioconductor's Annotation Libraries

Marc Carlson, Jianhua Zhang, Manvi Yaduvanshi

Rendered fromuseDataPkgs.Rmdusingknitr::rmarkdownon Nov 23 2025.

Last update: 2024-01-24
Started: 2024-01-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A function to convert accession values to NCBI UIDs.	accessionToUID
Provides statistics on the types of ids used for the ACCNUM environment of a given data package	ACCNUMStats whatACC
Get annotation package name from chip name	annPkgName
List GO Identifiers by GO Ontology	aqListGOIDs
Run a blast query to NCBI for either a string or an entrez gene ID and then return a series of MultipleAlignment objects.	blastSequences
A function to generate an instantiation of a chromLocation class	buildChromLocation
A function to generate an instantiation of a pubMedAbst class	buildPubMedAbst
Returns a list of chromosome locations from a MAP environment	chrCats createLLChrCats createMAPIncMat
Class chromLocation, a class for describing genes and their chromosome mappings.	chromInfo chromInfo,chromLocation-method chromLengths chromLengths,chromLocation-method chromLocation chromLocation-class chromLocs chromLocs,chromLocation-method chromNames chromNames,chromLocation-method dataSource dataSource,chromLocation-method geneSymbols geneSymbols,chromLocation-method nChrom nChrom,chromLocation-method organism,chromLocation-method probesToChrom probesToChrom,chromLocation-method show,chromLocation-method
function to check to see if the packages represented by the names passed have the same version number	compatibleVersions
Drop GO labels for specified Evidence Codes	dropECode
Create a Query String for an Entrez Gene Identifier	entrezGeneByID
Create a Query String for Entrez Genes	entrezGeneQuery
Filter GO terms by a specified GO ontology	filterGOByOntology
A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID	checkArgs findChr4LL findNeighbors getBoundary getValidChr weightByConfi
A function to open the browser to Genbank with the selected gene.	genbank
Get annotation map	getAnnMap
Get the Evidence codes for a set of GO terms.	getEvidence
Functions to Access GO data.	getGOChildren getGOOntology getGOParents getGOTerm
Get GO terms for a specified ontology	getOntology
extract publication details and abstract from annotate::pubmed function output	getPMInfo
Functions to create hypertext links that can be placed in a table cell of a HTML file	getCells getQuery4Affy getQuery4EN getQuery4ENSEMBL getQuery4FB getQuery4GB getQuery4OMIM getQuery4SP getQuery4TR getQuery4UG getQueryLink getTDRows
Queries the NCBI database to obtain the sequence for a given GenBank Accession number	getGI getSEQ
Functions to deal with Data Packages	getEG getGO getGOdesc getPMID getSYMBOL getUniqAnnItem lookUp
Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.	GO2heatmap KEGG2heatmap KEGG2heatmap,character,eSet,character-method KEGG2heatmap,character,matrix,character-method
A function to plot by group means against each other.	GOmnplot KEGGmnplot KEGGmnplot,character,eSet,character-method KEGGmnplot,character,matrix,character-method
Check for GO annotation	hasGOannote
A dataset to show the human genome base pair locations per chromosome.	hgByChroms
A dataset which contains the lengths (in base pairs) of the human chromosomes.	hgCLengths
Annotation data for the Affymetrix HGU95A GeneChip	hgu95Achroloc
Annotation data for the Affymetrix HGU95A GeneChip	hgu95Achrom
Annotation data for the Affymetrix HGU95A GeneChip	hgu95All
chromLocation instance hgu95AProbLocs, an example of a chromLocation object	hgu95AProbLocs
Annotation data for the Affymetrix HGU95A GeneChip	hgu95Asym
Class "homoData"	homoACC homoACC,homoData-method homoData homoData-class homoHGID homoHGID,homoData-method homoLL homoLL,homoData-method homoOrg homoOrg,homoData-method homoPS homoPS,homoData-method homoType homoType,homoData-method homoURL homoURL,homoData-method orgNameNCode show,homoData-method
Functions to build HTML pages	htmlpage
Classes to represent HTML pages	fileName fileName,HTMLPage-method FramedHTMLPage FramedHTMLPage,HTMLPage-method FramedHTMLPage-class HTMLPage HTMLPage,HTMLPage-method HTMLPage-class initialize,FramedHTMLPage-method mainPage mainPage,FramedHTMLPage-method mainPage,HTMLPage-method pageText pageText,HTMLPage-method pageTitle pageTitle,HTMLPage-method show,FramedHTMLPage-method show,HTMLPage-method sidePage sidePage,FramedHTMLPage-method sidePage,HTMLPage-method toFile toFile,FramedHTMLPage-method toFile,HTMLPage-method topPage topPage,FramedHTMLPage-method topPage,HTMLPage-method
Get or verify valid IDs for a package or OrgDb object.	allValidKeys allValidKeys,character-method allValidKeys,OrgDb-method isValidKey isValidKey,character,character-method isValidKey,character,OrgDb-method
DEFUNCT Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs	ACC2homology HGID2homology LL2homology
A Function To Generate HTML Anchors	makeAnchor
Functions to map to organism IDs used by NCBI homology.	getOrgNameNCode mapOrgs
Convenience function for getting the organism from an object or package	organism organism,character-method
An interface to grep for PubMed abstracts.	pm.abstGrep
Obtain the abstracts for a set PubMed list.	pm.getabst
Obtain the titles of the PubMed abstracts.	pm.titles
HTML Generation for PubMed Abstracts	pmAbst2HTML
use web to populate MIAME instance with pubmed details	pmid2MIAME
A function to compute the probe to PubMed id incidence matrix.	PMIDAmat
A function to query PubMed	pmidQuery
A function to open the browser to Pubmed with the selected gene.	pubmed
Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.	abstText abstText,pubMedAbst-method articleTitle articleTitle,pubMedAbst-method authors authors,pubMedAbst-method journal journal,pubMedAbst-method pmid pmid,pubMedAbst-method pubDate pubDate,pubMedAbst-method pubMedAbst pubMedAbst,pubMedAbst-method pubMedAbst-class show,pubMedAbst-method
A function to compute the probe to KEGG pathway incidence matrix.	PWAmat
Function to extract data from the GEO web site	getGPLNames getSAGEFileInfo getSAGEGPL readGEOAnn readIDNAcc readUrl
A Function To Serialize Environment	serializeDataPkgEnvs serializeEnv
Functions to add arbitrary repositories	clearRepository getRepositories setRepository
Create a Query String for a UniGene Identifier	UniGeneQuery
Take a list of symbols and translate them into the best possible ID for a package.	updateSymbolsToValidKeys
A function to select used genes on a chromosome from an ExpressionSet.	usedChromGenes

Package: annotate 1.89.0

annotate: Annotation for microarrays

Annotation Overview

Basic GO Usage

HowTo: Build and use chromosomal information

HowTo: Get HTML Output

HOWTO: Use the online query tools

Using Affymetrix Probe Level Data

Using Bioconductor's Annotation Libraries

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)