ACCNUMStats             Provides statistics on the types of ids used
                        for the ACCNUM environment of a given data
                        package
GO2heatmap              Compute a heatmap for the specified data, for
                        either a GO category or a KEGG pathway.
GOmnplot                A function to plot by group means against each
                        other.
HTMLPage-class          Classes to represent HTML pages
LL2homology             DEPRECATED Functions that find the homology
                        data for a given set of LocusLink ids or
                        HomoloGeneIDs
PMIDAmat                A function to compute the probe to PubMed id
                        incidence matrix.
PWAmat                  A function to compute the probe to KEGG pathway
                        incidence matrix.
UniGeneQuery            Create a Query String for a UniGene Identifier
accessionToUID          A function to convert accession values to NCBI
                        UIDs.
annPkgName              Get annotation package name from chip name
annotate-defunct        Defunct Functions in Package 'annotate'
aqListGOIDs             List GO Identifiers by GO Ontology
blastSequences          Run a blast query to NCBI for either a string
                        or an entrez gene ID and then return a series
                        of MultipleAlignment objects.
buildChromLocation      A function to generate an instantiation of a
                        chromLocation class
buildPubMedAbst         A function to generate an instantiation of a
                        pubMedAbst class
chrCats                 Returns a list of chromosome locations from a
                        MAP environment
chromLocation-class     Class chromLocation, a class for describing
                        genes and their chromosome mappings.
compatibleVersions      function to check to see if the packages
                        represented by the names passed have the same
                        version number
dropECode               Drop GO labels for specified Evidence Codes
entrezGeneByID          Create a Query String for an Entrez Gene
                        Identifier
entrezGeneQuery         Create a Query String for Entrez Genes
filterGOByOntology      Filter GO terms by a specified GO ontology
findNeighbors           A function to locate neighboring genes within a
                        defined range around a target gene represented
                        by a Entrez Gene ID
genbank                 A function to open the browser to Genbank with
                        the selected gene.
getAnnMap               Get annotation map
getEvidence             Get the Evidence codes for a set of GO terms.
getGOTerm               Functions to Access GO data.
getOntology             Get GO terms for a specified ontology
getPMInfo               extract publication details and abstract from
                        annotate::pubmed function output
getQueryLink            Functions to create hypertext links that can be
                        placed in a table cell of a HTML file
getSEQ                  Queries the NCBI database to obtain the
                        sequence for a given GenBank Accession number
getSYMBOL               Functions to deal with Data Packages
hasGOannote             Check for GO annotation
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
homoData-class          Class "homoData"
htmlpage                Functions to build HTML pages
isValidKey              Get or verify valid IDs for a package.
makeAnchor              A Function To Generate HTML Anchors
mapOrgs                 Functions to map to organism IDs used by NCBI
                        homology.
organism                Convenience function for getting the organism
                        from an object or package
p2LL                    A function to map from probes to unique Entrez
                        Gene IDs
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
pmid2MIAME              use web to populate MIAME instance with pubmed
                        details
pmidQuery               A function to query PubMed
pubMedAbst-class        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.
readGEOAnn              Function to extract data from the GEO web site
serializeEnv            A Function To Serialize Environment
setRepository           Functions to add arbitrary repositories
updateSymbolsToValidKeys
                        Take a list of symbols and translate them into
                        the best possible ID for a package.
usedChromGenes          A function to select used genes on a chromosome
                        from an ExpressionSet.