Entry: ACCNUMStats
Aliases: ACCNUMStats whatACC
Keywords: misc
Description: Provides statistics on the types of ids used for the ACCNUM environment of a given data package
URL: ../../../library/annotate/html/ACCNUMStats.html

Entry: GO2heatmap
Aliases: GO2heatmap KEGG2heatmap KEGG2heatmap,character,eSet,character-method KEGG2heatmap,character,matrix,character-method
Keywords: manip
Description: Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
URL: ../../../library/annotate/html/GO2heatmap.html

Entry: GOTerms-class
Aliases: GOTerms GOID Ontology Definition Term Secondary Synonym GOTerms-class Ontology,GOTerms-method Ontology,ANY-method Definition,GOTerms-method GOID,GOTerms-method Term,GOTerms-method Secondary,GOTerms-method Synonym,GOTerms-method show,GOTerms-method
Keywords: classes
Description: Class "GOTerms"
URL: ../../../library/annotate/html/GOTerms-class.html

Entry: GOmnplot
Aliases: GOmnplot KEGGmnplot KEGGmnplot,character,eSet,character-method KEGGmnplot,character,matrix,character-method
Keywords: manip
Description: A function to plot by group means against each other.
URL: ../../../library/annotate/html/GOmnplot.html

Entry: HTMLPage-class
Aliases: HTMLPage-class HTMLPage FramedHTMLPage FramedHTMLPage-class fileName mainPage sidePage pageText toFile topPage pageTitle HTMLPage,HTMLPage-method FramedHTMLPage,HTMLPage-method fileName,HTMLPage-method mainPage,HTMLPage-method sidePage,HTMLPage-method pageText,HTMLPage-method toFile,HTMLPage-method topPage,HTMLPage-method pageTitle,HTMLPage-method show,HTMLPage-method initialize,FramedHTMLPage-method mainPage,FramedHTMLPage-method show,FramedHTMLPage-method sidePage,FramedHTMLPage-method toFile,FramedHTMLPage-method topPage,FramedHTMLPage-method
Keywords: classes
Description: Classes to represent HTML pages
URL: ../../../library/annotate/html/HTMLPage-class.html

Entry: LL2homology
Aliases: LL2homology HGID2homology ACC2homology
Keywords: misc
Description: Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
URL: ../../../library/annotate/html/LL2homology.html

Entry: PMIDAmat
Aliases: PMIDAmat
Keywords: manip
Description: A function to compute the probe to PubMed id incidence matrix.
URL: ../../../library/annotate/html/PMIDAmat.html

Entry: PWAmat
Aliases: PWAmat
Keywords: manip
Description: A function to compute the probe to KEGG pathway incidence matrix.
URL: ../../../library/annotate/html/PWAmat.html

Entry: UniGeneQuery
Aliases: UniGeneQuery
Keywords: interface
Description: Create a Query String for a UniGene Identifier
URL: ../../../library/annotate/html/UniGeneQuery.html

Entry: accessionToUID
Aliases: accessionToUID
Keywords: interface
Description: A function to convert accession values to NCBI UIDs.
URL: ../../../library/annotate/html/accessionToUID.html

Entry: buildChromLocation
Aliases: buildChromLocation
Keywords: utilities
Description: A function to generate an instantiation of a chromLocation class
URL: ../../../library/annotate/html/buildChromLocation.html

Entry: buildPubMedAbst
Aliases: buildPubMedAbst
Keywords: utilities
Description: A function to generate an instantiation of a pubMedAbst class
URL: ../../../library/annotate/html/buildPubMedAbst.html

Entry: chrCats
Aliases: chrCats createLLChrCats createMAPIncMat
Keywords: data
Description: Returns a list of chromosome locations from a MAP environment
URL: ../../../library/annotate/html/chrCats.html

Entry: chromLocation-class
Aliases: chromLocation-class organism dataSource nChrom chromNames chromLocs chromLengths probesToChrom geneSymbols chromInfo organism,chromLocation-method dataSource,chromLocation-method nChrom,chromLocation-method chromNames,chromLocation-method chromLocs,chromLocation-method chromLengths,chromLocation-method probesToChrom,chromLocation-method geneSymbols,chromLocation-method chromInfo,chromLocation-method show,chromLocation-method
Keywords: classes
Description: Class chromLocation, a class for describing genes and their chromosome mappings.
URL: ../../../library/annotate/html/chromLocation-class.html

Entry: compatibleVersions
Aliases: compatibleVersions
Keywords: misc
Description: function to check to see if the packages represented by the names passed have the same version number
URL: ../../../library/annotate/html/compatibleVersions.html

Entry: dropECode
Aliases: dropECode
Keywords: manip
Description: Drop GO labels for specified Evidence Codes
URL: ../../../library/annotate/html/dropECode.html

Entry: findNeighbors
Aliases: findNeighbors checkArgs findChr4LL getValidChr getBoundary weightByConfi
Keywords: manip
Description: A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id
URL: ../../../library/annotate/html/findNeighbors.html

Entry: genbank
Aliases: genbank
Keywords: interface
Description: A function to open the browser to Genbank with the selected gene.
URL: ../../../library/annotate/html/genbank.html

Entry: genelocator
Aliases: genelocator
Keywords: iplot
Description: A function to identify genes by their LocusLink (or other id).
URL: ../../../library/annotate/html/genelocator.html

Entry: getEvidence
Aliases: getEvidence
Keywords: manip
Description: Get the Evidence codes for a set of GO terms.
URL: ../../../library/annotate/html/getEvidence.html

Entry: getGOTerm
Aliases: getGOTerm getGOParents getGOChildren getGOOntology
Keywords: manip
Description: Functions to Access GO data.
URL: ../../../library/annotate/html/getGOTerm.html

Entry: getOntology
Aliases: getOntology
Keywords: manip
Description: Get GO terms for a specified ontology
URL: ../../../library/annotate/html/getOntology.html

Entry: getPMInfo
Aliases: getPMInfo
Keywords: models
Description: extract publication details and abstract from annotate::pubmed function output
URL: ../../../library/annotate/html/getPMInfo.html

Entry: getSYMBOL
Aliases: getSYMBOL getGO getGOdesc getPMID getLL lookUp getUniqAnnItem
Keywords: manip
Description: Functions to deal with Data Packages
URL: ../../../library/annotate/html/getSYMBOL.html

Entry: getSEQ
Aliases: getGI getSEQ
Keywords: misc
Description: Queries the NCBI database to obtain the sequence for a given GenBank Accession number
URL: ../../../library/annotate/html/getSeq4Acc.html

Entry: getQueryLink
Aliases: getQueryLink getQuery4UG getQuery4SP getQuery4OMIM getQuery4LL getQuery4GB getQuery4Affy getQuery4FB getQuery4EN getCells getTDRows
Keywords: manip
Description: Functions to create hypertext links that can be placed in a table cell of a HTML file
URL: ../../../library/annotate/html/getTDRows.html

Entry: hasGOannote
Aliases: hasGOannote
Keywords: manip
Description: Check for GO annotation
URL: ../../../library/annotate/html/hasGOannote.html

Entry: hgByChroms
Aliases: hgByChroms
Keywords: datasets
Description: A dataset to show the human genome base pair locations per chromosome.
URL: ../../../library/annotate/html/hgByChroms.html

Entry: hgCLengths
Aliases: hgCLengths
Keywords: datasets
Description: A dataset which contains the lengths (in base pairs) of the human chromosomes.
URL: ../../../library/annotate/html/hgCLengths.html

Entry: hgu95AProbLocs
Aliases: hgu95AProbLocs
Keywords: methods
Description: chromLocation instance hgu95AProbLocs, an example of a chromLocation object
URL: ../../../library/annotate/html/hgu95AProbLocs.html

Entry: hgu95Achroloc
Aliases: hgu95Achroloc
Keywords: datasets
Description: Annotation data for the Affymetrix HGU95A GeneChip
URL: ../../../library/annotate/html/hgu95Achroloc.html

Entry: hgu95Achrom
Aliases: hgu95Achrom
Keywords: datasets
Description: Annotation data for the Affymetrix HGU95A GeneChip
URL: ../../../library/annotate/html/hgu95Achrom.html

Entry: hgu95All
Aliases: hgu95All
Keywords: datasets
Description: Annotation data for the Affymetrix HGU95A GeneChip
URL: ../../../library/annotate/html/hgu95All.html

Entry: hgu95Asym
Aliases: hgu95Asym
Keywords: datasets
Description: Annotation data for the Affymetrix HGU95A GeneChip
URL: ../../../library/annotate/html/hgu95Asym.html

Entry: homoData-class
Aliases: homoData-class homoData homoLL homoOrg homoType homoURL homoACC homoHGID homoPS orgNameNCode homoPS,homoData-method homoLL,homoData-method homoOrg,homoData-method homoType,homoData-method homoURL,homoData-method homoACC,homoData-method homoHGID,homoData-method show,homoData-method
Keywords: classes
Description: Class "homoData"
URL: ../../../library/annotate/html/homoData-class.html

Entry: htmlpage
Aliases: htmlpage
Keywords: manip
Description: Functions to build HTML pages
URL: ../../../library/annotate/html/htmlpage.html

Entry: installDataPackage
Aliases: installDataPackage
Keywords: utilities
Description: A function to install data packages from the Internet
URL: ../../../library/annotate/html/installDataPackage.html

Entry: locuslinkByID
Aliases: locuslinkByID
Keywords: interface
Description: A function to open the browser to Locuslink with the selected gene.
URL: ../../../library/annotate/html/locuslinkById.html

Entry: locuslinkQuery
Aliases: locuslinkQuery
Keywords: interface
Description: A function to open the browser to Locuslink using a provided search query.
URL: ../../../library/annotate/html/locuslinkQuery.html

Entry: makeAnchor
Aliases: makeAnchor
Keywords: utilities
Description: A Function To Generate HTML Anchors
URL: ../../../library/annotate/html/makeAnchor.html

Entry: neighborGeneFinder
Aliases: neighborGeneFinder
Keywords: interface
Description: A widget for locating genes neighboring a target gene
URL: ../../../library/annotate/html/neighborGeneFinder.html

Entry: p2LL
Aliases: p2LL
Keywords: manip
Description: A function to map from probes to unique Entrez Gene IDs
URL: ../../../library/annotate/html/p2LL.html

Entry: pm.abstGrep
Aliases: pm.abstGrep
Keywords: manip
Description: An interface to grep for PubMed abstracts.
URL: ../../../library/annotate/html/pm.abstGrep.html

Entry: pm.getabst
Aliases: pm.getabst
Keywords: manip
Description: Obtain the abstracts for a set PubMed list.
URL: ../../../library/annotate/html/pm.getabst.html

Entry: pm.titles
Aliases: pm.titles
Keywords: manip
Description: Obtain the titles of the PubMed abstracts.
URL: ../../../library/annotate/html/pm.titles.html

Entry: pmAbst2HTML
Aliases: pmAbst2HTML
Keywords: utilities
Description: HTML Generation for PubMed Abstracts
URL: ../../../library/annotate/html/pmAbst2HTML.html

Entry: pmid2MIAME
Aliases: pmid2MIAME
Keywords: models
Description: use web to populate MIAME instance with pubmed details
URL: ../../../library/annotate/html/pmid2MIAME.html

Entry: pmidQuery
Aliases: pmidQuery
Keywords: interface
Description: A function to query PubMed
URL: ../../../library/annotate/html/pmidQuery.html

Entry: probesByLL
Aliases: probesByLL
Keywords: manip
Description: A function that does reverse the mappings between probe ids and the corresponding values
URL: ../../../library/annotate/html/probesByLL.html

Entry: pubMedAbst-class
Aliases: pubMedAbst-class pubMedAbst authors abstText articleTitle journal pubDate abstUrl pmid pubMedAbst,pubMedAbst-method authors,pubMedAbst-method abstText,pubMedAbst-method articleTitle,pubMedAbst-method journal,pubMedAbst-method pubDate,pubMedAbst-method abstUrl,pubMedAbst-method pmid,pubMedAbst-method show,pubMedAbst-method
Keywords: classes
Description: Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
URL: ../../../library/annotate/html/pubMedAbst-class.html

Entry: pubmed
Aliases: pubmed
Keywords: interface
Description: A function to open the browser to Pubmed with the selected gene.
URL: ../../../library/annotate/html/pubmed.html

Entry: readGEOAnn
Aliases: readGEOAnn readIDNAcc getGPLNames getSAGEFileInfo getSAGEGPL readUrl
Keywords: manip
Description: Function to extract data from the GEO web site
URL: ../../../library/annotate/html/readGEOAnn.html

Entry: serializeEnv
Aliases: serializeEnv serializeDataPkgEnvs
Keywords: utilities
Description: A Function To Serialize Environment
URL: ../../../library/annotate/html/serializeEnv.html

Entry: usedChromGenes
Aliases: usedChromGenes
Keywords: interface
Description: A function to select used genes on a chromosome from an exprSet.
URL: ../../../library/annotate/html/usedChromGenes.html