| abstText |
Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them. |
| abstText,pubMedAbst-method |
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. |
| abstUrl,pubMedAbst-method |
Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them. |
| ACC2homology |
Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs |
| 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 |
| articleTitle |
Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them. |
| articleTitle,pubMedAbst-method |
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. |
| authors,pubMedAbst-method |
Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them. |
| checkArgs |
A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id |
| chrCats |
Returns a list of chromosome locations from a MAP environment |
| chromInfo |
Class chromLocation, a class for describing genes and their chromosome mappings. |
| chromInfo,chromLocation-method |
Class chromLocation, a class for describing genes and their chromosome mappings. |
| chromLengths |
Class chromLocation, a class for describing genes and their chromosome mappings. |
| chromLengths,chromLocation-method |
Class chromLocation, a class for describing genes and their chromosome mappings. |
| 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. |
| chromLocs,chromLocation-method |
Class chromLocation, a class for describing genes and their chromosome mappings. |
| chromNames |
Class chromLocation, a class for describing genes and their chromosome mappings. |
| chromNames,chromLocation-method |
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 |
| createLLChrCats |
Returns a list of chromosome locations from a MAP environment |
| createMAPIncMat |
Returns a list of chromosome locations from a MAP environment |
| 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. |
| geneSymbols,chromLocation-method |
Class chromLocation, a class for describing genes and their chromosome mappings. |
| getBoundary |
A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id |
| getCells |
Functions to create hypertext links that can be placed in a table cell of a HTML file |
| getEvidence |
Get the Evidence codes for a set of GO terms. |
| getGI |
Queries the NCBI database to obtain the sequence for a given GenBank Accession number |
| getGO |
Functions to deal with Data Packages |
| getGOChildren |
Functions to Access GO data. |
| getGOdesc |
Functions to deal with Data Packages |
| getGOOntology |
Functions to Access GO data. |
| getGOParents |
Functions to Access GO data. |
| getGOTerm |
Functions to Access GO data. |
| getGPLNames |
Function to extract data from the GEO web site |
| getLL |
Functions to deal with Data Packages |
| getOntology |
Get GO terms for a specified ontology |
| getPMID |
Functions to deal with Data Packages |
| getPMInfo |
extract publication details and abstract from annotate::pubmed function output |
| getQuery4Affy |
Functions to create hypertext links that can be placed in a table cell of a HTML file |
| getQuery4EN |
Functions to create hypertext links that can be placed in a table cell of a HTML file |
| getQuery4FB |
Functions to create hypertext links that can be placed in a table cell of a HTML file |
| getQuery4GB |
Functions to create hypertext links that can be placed in a table cell of a HTML file |
| getQuery4LL |
Functions to create hypertext links that can be placed in a table cell of a HTML file |
| getQuery4OMIM |
Functions to create hypertext links that can be placed in a table cell of a HTML file |
| getQuery4SP |
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 |
| getSAGEFileInfo |
Function to extract data from the GEO web site |
| getSAGEGPL |
Function to extract data from the GEO web site |
| getSEQ |
Queries the NCBI database to obtain the sequence for a given GenBank Accession number |
| 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 |
| getUniqAnnItem |
Functions to deal with Data Packages |
| getValidChr |
A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id |
| GO2heatmap |
Compute a heatmap for the specified data, for either a GO category or a KEGG pathway. |
| GOID |
Class "GOTerms" |
| GOID,GOTerms-method |
Class "GOTerms" |
| GOmnplot |
A function to plot by group means against each other. |
| GOTerms |
Class "GOTerms" |
| GOTerms-class |
Class "GOTerms" |
| KEGG2heatmap |
Compute a heatmap for the specified data, for either a GO category or a KEGG pathway. |
| KEGG2heatmap,character,eSet,character-method |
Compute a heatmap for the specified data, for either a GO category or a KEGG pathway. |
| KEGG2heatmap,character,matrix,character-method |
Compute a heatmap for the specified data, for either a GO category or a KEGG pathway. |
| KEGGmnplot |
A function to plot by group means against each other. |
| KEGGmnplot,character,eSet,character-method |
A function to plot by group means against each other. |
| KEGGmnplot,character,matrix,character-method |
A function to plot by group means against each other. |
| p2LL |
A function to map from probes to unique Entrez Gene IDs |
| pageText |
Classes to represent HTML pages |
| pageText,HTMLPage-method |
Classes to represent HTML pages |
| pageTitle |
Classes to represent HTML pages |
| pageTitle,HTMLPage-method |
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 |
| pmid |
Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them. |
| pmid,pubMedAbst-method |
Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them. |
| pmid2MIAME |
use web to populate MIAME instance with pubmed details |
| PMIDAmat |
A function to compute the probe to PubMed id incidence matrix. |
| pmidQuery |
A function to query PubMed |
| probesByLL |
A function that does reverse the mappings between probe ids and the corresponding values |
| probesToChrom |
Class chromLocation, a class for describing genes and their chromosome mappings. |
| probesToChrom,chromLocation-method |
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. |
| pubDate,pubMedAbst-method |
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,pubMedAbst-method |
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. |
| PWAmat |
A function to compute the probe to KEGG pathway incidence matrix. |
| Secondary |
Class "GOTerms" |
| Secondary,GOTerms-method |
Class "GOTerms" |
| serializeDataPkgEnvs |
A Function To Serialize Environment |
| serializeEnv |
A Function To Serialize Environment |
| show,chromLocation-method |
Class chromLocation, a class for describing genes and their chromosome mappings. |
| show,FramedHTMLPage-method |
Classes to represent HTML pages |
| show,GOTerms-method |
Class "GOTerms" |
| show,homoData-method |
Class "homoData" |
| show,HTMLPage-method |
Classes to represent HTML pages |
| show,pubMedAbst-method |
Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them. |
| sidePage |
Classes to represent HTML pages |
| sidePage,FramedHTMLPage-method |
Classes to represent HTML pages |
| sidePage,HTMLPage-method |
Classes to represent HTML pages |
| Synonym |
Class "GOTerms" |
| Synonym,GOTerms-method |
Class "GOTerms" |