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 CHRLOC2chromLoc
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: 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: 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: 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 contents contents,environment-method
Keywords: manip
Description: Functions to deal with Data Packages
URL: ../../../library/annotate/html/getSYMBOL.html

Entry: getTDRows
Aliases: getTDRows getQueryLink getQuery4UG getQuery4LL
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: 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: hgu95Achroloc
Aliases: hgu95Achroloc
Keywords: datasets
Description: Annotation data for the Affymetrix HGU95A GeneChip
URL: ../../../library/annotate/html/hgu95Achroloc.html

Entry: hgu95Achrom
Aliases: hgu95Achrom hgu95AchromNames
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: hgu95AProbLocs
Aliases: hgu95AProbLocs
Keywords: methods
Description: chromLocation instance hgu95AProbLocs, an example of a chromLocation object
URL: ../../../library/annotate/html/hgu95AProbLocs.html

Entry: hgu95Asym
Aliases: hgu95Asym
Keywords: datasets
Description: Annotation data for the Affymetrix HGU95A GeneChip
URL: ../../../library/annotate/html/hgu95Asym.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: installDataPackage
Aliases: installDataPackage
Keywords: utilities
Description: A function to install data packages from the Internet
URL: ../../../library/annotate/html/installDataPackage.html

Entry: ll.htmlpage
Aliases: ll.htmlpage
Keywords: file 
Description: Turn LocusLink ID's into a Clickable Web Page
URL: ../../../library/annotate/html/ll.htmlpage.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: 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 pmAbst2html2
Keywords: utilities
Description: HTML Generation for PubMed Abstracts
URL: ../../../library/annotate/html/pmAbst2HTML.html

Entry: pmidQuery
Aliases: pmidQuery
Keywords: interface
Description: A function to query PubMed
URL: ../../../library/annotate/html/pmidQuery.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: 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: UniGeneQuery
Aliases: UniGeneQuery
Keywords: interface
Description: Create a Query String for a UniGene Identifier
URL: ../../../library/annotate/html/UniGeneQuery.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
