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 |
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 |
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 |
getGI |
Queries the NCBI database to obtain the sequence for a given GenBank Accession number |
getGO |
Functions to deal with Data Packages |
getGOdesc |
Functions to deal with Data Packages |
getGPLNames |
Function to extract data from the GEO web site |
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 |
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" |
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" |