| accessionToUID | A function to convert accession values to NCBI UIDs. |
| ACCNUMStats | Provides statistics on the types of ids used for the ACCNUM... |
| annotate-defunct | Defunct Functions in Package 'annotate' |
| annPkgName | Get annotation package name from chip name |
| aqListGOIDs | List GO Identifiers by GO Ontology |
| blastSequences | Run a blast query to NCBI for either a string or an entrez... |
| buildChromLocation | A function to generate an instantiation of a chromLocation... |
| 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... |
| compatibleVersions | function to check to see if the packages represented by the... |
| 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... |
| genbank | A function to open the browser to Genbank with the selected... |
| 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... |
| getSeq4Acc | Queries the NCBI database to obtain the sequence for a given... |
| getSYMBOL | Functions to deal with Data Packages |
| getTDRows | Functions to create hypertext links that can be placed in a... |
| GO2heatmap | Compute a heatmap for the specified data, for either a GO... |
| GOmnplot | A function to plot by group means against each other. |
| hasGOannote | Check for GO annotation |
| hgByChroms | A dataset to show the human genome base pair locations per... |
| hgCLengths | A dataset which contains the lengths (in base pairs) of the... |
| 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... |
| 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 |
| isValidkey | Get or verify valid IDs for a package or OrgDb object. |
| LL2homology | DEPRECATED Functions that find the homology data for a given... |
| 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... |
| 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. |
| pmid2MIAME | use web to populate MIAME instance with pubmed details |
| PMIDAmat | A function to compute the probe to PubMed id incidence... |
| pmidQuery | A function to query PubMed |
| pm.titles | Obtain the titles of the PubMed abstracts. |
| pubmed | A function to open the browser to Pubmed with the selected... |
| pubMedAbst-class | Class pubMedAbst, a class to handle PubMed abstracts, and... |
| PWAmat | A function to compute the probe to KEGG pathway incidence... |
| readGEOAnn | Function to extract data from the GEO web site |
| serializeEnv | A Function To Serialize Environment |
| setRepository | Functions to add arbitrary repositories |
| UniGeneQuery | Create a Query String for a UniGene Identifier |
| updateSymbolsToValidKeys | Take a list of symbols and translate them into the best... |
| usedChromGenes | A function to select used genes on a chromosome from an... |
