| Function | Description |
| accessionToUID | A function to convert accession values to NCBI UIDs. |
| ACCNUMStats | Provides statistics on the types of ids used for the ACCNUM environment of a given data package |
| buildChromLocation | A function to generate an instantiation of a chromLocation class |
| buildPubMedAbst | A function to generate an instantiation of a pubMedAbst class |
| 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 |
| findNeighbors | A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id |
| 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). |
| 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 |
| 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. |
| GOTerms-class | Class "GOTerms" |
| 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 |
| 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 |
| homoData-class | Class "homoData" |
| htmlpage | Functions to build HTML pages |
| HTMLPage-class | Classes to represent HTML pages |
| installDataPackage | A function to install data packages from the Internet |
| LL2homology | Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs |
| 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. |
| makeAnchor | A Function To Generate HTML Anchors |
| neighborGeneFinder | A widget for locating genes neighboring a target gene |
| p2LL | A function to map from probes to unique Entrez Gene IDs |
| pmAbst2HTML | HTML Generation for PubMed Abstracts |
| pm.abstGrep | An interface to grep for PubMed abstracts. |
| pm.getabst | Obtain the abstracts for a set PubMed list. |
| pmidQuery | A function to query PubMed |
| pm.titles | Obtain the titles of the PubMed abstracts. |
| probesByLL | A function that does reverse the mappings between probe ids and the corresponding values |
| pubmed | A function to open the browser to Pubmed with the selected gene. |
| pubMedAbst-class | Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them. |
| PWAmat | A function to compute the probe to KEGG pathway incidence matrix. |
| readGEOAnn | Function to extract data from the GEO web site |
| revString | Functions to create anti-sense DNA string |
| serializeEnv | A Function To Serialize Environment |
| UniGeneQuery | Create a Query String for a UniGene Identifier |
| usedChromGenes | A function to select used genes on a chromosome from an exprSet. |