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Accompanying documentation is available in the subdirectory "doc" of the installed package.

abstText Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
abstUrl Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
accessionToUID A function to convert accession values to NCBI UIDs.
articleTitle Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
authors Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
buildChromLocation A function to generate an instantiation of a chromLocation class
buildPubMedAbst A function to generate an instantiation of a pubMedAbst class
CHRLOC2chromLoc A function to generate an instantiation of a chromLocation class
chrom Class chromLoc, a class for describing the location of a gene on a chromosome.
chromInfo Class chromLocation, a class for describing genes and their chromosome mappings.
chromLengths Class chromLocation, a class for describing genes and their chromosome mappings.
chromLoc Class chromLoc, a class for describing the location of a gene on a chromosome.
chromLoc-class Class chromLoc, a class for describing the location of a gene on a chromosome.
chromLocation-class Class chromLocation, a class for describing genes and their chromosome mappings.
chromLocs Class chromLocation, a class for describing genes and their chromosome mappings.
chromNames Class chromLocation, a class for describing genes and their chromosome mappings.
contents Functions to deal with Data Packages
dataSource Class chromLocation, a class for describing genes and their chromosome mappings.
fileName Classes to represent HTML pages
FramedHTMLPage Classes to represent HTML pages
FramedHTMLPage-class Classes to represent HTML pages
genbank A function to open the browser to Genbank with the selected gene.
genelocator A function to identify genes by their LocusLink (or other id).
geneSymbols Class chromLocation, a class for describing genes and their chromosome mappings.
getGO Functions to deal with Data Packages
getGOdesc Functions to deal with Data Packages
getLL Functions to deal with Data Packages
getPMID Functions to deal with Data Packages
getPMInfo extract publication details and abstract from annotate::pubmed function output
getQuery4LL Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4UG Functions to create hypertext links that can be placed in a table cell of a HTML file
getQueryLink Functions to create hypertext links that can be placed in a table cell of a HTML file
getSYMBOL Functions to deal with Data Packages
getTDRows Functions to create hypertext links that can be placed in a table cell of a HTML file
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.
hgu95Achroloc Annotation data for the Affymetrix HGU95A GeneChip
hgu95Achrom Annotation data for the Affymetrix HGU95A GeneChip
hgu95AchromNames Annotation data for the Affymetrix HGU95A GeneChip
hgu95All Annotation data for the Affymetrix HGU95A GeneChip
hgu95AProbLocs chromLocation instance hgu95AProbLocs, an example of a chromLocation object
hgu95Asym Annotation data for the Affymetrix HGU95A GeneChip
HTMLPage Classes to represent HTML pages
HTMLPage-class Classes to represent HTML pages
installDataPackage A function to install data packages from the Internet
journal Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
ll.htmlpage Turn LocusLink ID's into a Clickable Web Page
locuslinkByID A function to open the browser to Locuslink with the selected gene.
locuslinkQuery A function to open the browser to Locuslink using a provided search query.
mainPage Classes to represent HTML pages
makeAnchor A Function To Generate HTML Anchors
nChrom Class chromLocation, a class for describing genes and their chromosome mappings.
organism Class chromLocation, a class for describing genes and their chromosome mappings.
pageText Classes to represent HTML pages
pageTitle Classes to represent HTML pages
pm.abstGrep An interface to grep for PubMed abstracts.
pm.getabst Obtain the abstracts for a set PubMed list.
pm.titles Obtain the titles of the PubMed abstracts.
pmAbst2HTML HTML Generation for PubMed Abstracts
pmAbst2html2 HTML Generation for PubMed Abstracts
pmid Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pmidQuery A function to query PubMed
position Class chromLoc, a class for describing the location of a gene on a chromosome.
probesToChrom Class chromLocation, a class for describing genes and their chromosome mappings.
pubDate Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubmed A function to open the browser to Pubmed with the selected gene.
pubMedAbst Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubMedAbst-class Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
sidePage Classes to represent HTML pages
strand Class chromLoc, a class for describing the location of a gene on a chromosome.
toFile Classes to represent HTML pages
topPage Classes to represent HTML pages
UniGeneQuery Create a Query String for a UniGene Identifier
usedChromGenes A function to select used genes on a chromosome from an exprSet.