Package: annotate 1.85.0

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'))

Peer review:

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-1.85.0(bioc 3.21)annotate-1.84.0(bioc 3.20)

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

annotationpathwaysgo

11.74 score 254 packages 792 scripts 32k downloads 36 mentions 126 exports 41 dependencies

Last updated 2 months agofrom:732426ec76. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winERRORNov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winERRORNov 29 2024
R-4.3-macNOTENov 29 2024

Exports:.buildAnnotateOpts.efetch.getIdTag.getNcbiURL.handleXML.transformAccessionabstTextACC2homologyaccessionToUIDACCNUMStatsallValidKeysannPkgNameaqListGOIDsarticleTitleauthorsblastSequencesbuildChromLocationbuildPubMedAbstcheckArgschrCatschromInfochromLengthschromLocschromNamesclearRepositorycompatibleVersionscreateLLChrCatscreateMAPIncMatdataSourceDefinitiondropECodeentrezGeneByIDentrezGeneQueryfileNamefilterGOByOntologyfindChr4LLfindNeighborsgenbankgeneSymbolsgetAnnMapgetBoundarygetEGgetEvidencegetGIgetGOgetGOChildrengetGOdescgetGOOntologygetGOParentsgetGOTermgetGPLNamesgetLLgetOntologygetOrgNameNCodegetPMIDgetPMInfogetQueryLinkgetRepositoriesgetSAGEFileInfogetSAGEGPLgetSEQgetSYMBOLgetUniqAnnItemgetValidChrGO2heatmapGOIDGOmnplothasGOannoteHGID2homologyhomoACChomoDatahomoHGIDhomoLLhomoOrghomoPShomoTypehomoURLhtmlpageinitializeisValidKeyjournalKEGG2heatmapKEGGmnplotLL2homologylookUpmainPagemakeAnchormapOrgsnChromOntologyorganismp2LLpageTextpageTitlepm.abstGreppm.getabstpm.titlespmAbst2HTMLpmidpmid2MIAMEPMIDAmatpmidQueryprobesByLLprobesToChrompubDatepubmedpubMedAbstPWAmatreadGEOAnnreadIDNAccreadUrlSecondaryserializeDataPkgEnvsserializeEnvsetRepositoryshowsidePageSynonymTermtoFiletopPageUniGeneQueryupdateSymbolsToValidKeysusedChromGenesweightByConfiwhatACC

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorssysUCSC.utilsvctrsXMLxtableXVectorzlibbioc

Annotation Overview

Rendered fromannotate.Rnwusingutils::Sweaveon Nov 29 2024.

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

Basic GO Usage

Rendered fromGOusage.Rnwusingutils::Sweaveon Nov 29 2024.

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

HowTo: Build and use chromosomal information

Jeff Gentry, Kritika Verma

Rendered fromchromLOC.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

HowTo: Get HTML Output

Rendered fromprettyOutput.Rnwusingutils::Sweaveon Nov 29 2024.

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

HOWTO: Use the online query tools

Rendered fromquery.Rnwusingutils::Sweaveon Nov 29 2024.

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

Using Affymetrix Probe Level Data

Rendered fromuseProbeInfo.Rnwusingutils::Sweaveon Nov 29 2024.

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 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
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 packageACCNUMStats whatACC
Defunct Functions in Package 'annotate'annotate-defunct genelocator getQuery4LL neighborGeneFinder probesByLL
Get annotation package name from chip nameannPkgName
List GO Identifiers by GO OntologyaqListGOIDs
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 classbuildChromLocation
A function to generate an instantiation of a pubMedAbst classbuildPubMedAbst
Returns a list of chromosome locations from a MAP environmentchrCats 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 numbercompatibleVersions
Drop GO labels for specified Evidence CodesdropECode
Create a Query String for an Entrez Gene IdentifierentrezGeneByID
Create a Query String for Entrez GenesentrezGeneQuery
Filter GO terms by a specified GO ontologyfilterGOByOntology
A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene IDcheckArgs findChr4LL findNeighbors getBoundary getValidChr weightByConfi
A function to open the browser to Genbank with the selected gene.genbank
Get annotation mapgetAnnMap
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 ontologygetOntology
extract publication details and abstract from annotate::pubmed function outputgetPMInfo
Functions to create hypertext links that can be placed in a table cell of a HTML filegetCells getQuery4Affy getQuery4EN getQuery4ENSEMBL getQuery4FB getQuery4GB getQuery4OMIM getQuery4SP getQuery4TR getQuery4UG getQueryLink getTDRows
Queries the NCBI database to obtain the sequence for a given GenBank Accession numbergetGI getSEQ
Functions to deal with Data PackagesgetEG getGO getGOdesc getLL 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 annotationhasGOannote
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 GeneChiphgu95Achroloc
Annotation data for the Affymetrix HGU95A GeneChiphgu95Achrom
Annotation data for the Affymetrix HGU95A GeneChiphgu95All
chromLocation instance hgu95AProbLocs, an example of a chromLocation objecthgu95AProbLocs
Annotation data for the Affymetrix HGU95A GeneChiphgu95Asym
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 pageshtmlpage
Classes to represent HTML pagesfileName 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
DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDsACC2homology HGID2homology LL2homology
A Function To Generate HTML AnchorsmakeAnchor
Functions to map to organism IDs used by NCBI homology.getOrgNameNCode mapOrgs
Convenience function for getting the organism from an object or packageorganism organism,character-method
A function to map from probes to unique Entrez Gene IDsp2LL
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 AbstractspmAbst2HTML
use web to populate MIAME instance with pubmed detailspmid2MIAME
A function to compute the probe to PubMed id incidence matrix.PMIDAmat
A function to query PubMedpmidQuery
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 sitegetGPLNames getSAGEFileInfo getSAGEGPL readGEOAnn readIDNAcc readUrl
A Function To Serialize EnvironmentserializeDataPkgEnvs serializeEnv
Functions to add arbitrary repositoriesclearRepository getRepositories setRepository
Create a Query String for a UniGene IdentifierUniGeneQuery
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