annotate

Provides statistics on the types of ids used for the ACCNUM environment of a given data package

Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.

A function to plot by group means against each other.

Classes to represent HTML pages

DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs

A function to compute the probe to PubMed id incidence matrix.

A function to compute the probe to KEGG pathway incidence matrix.

Create a Query String for a UniGene Identifier

A function to convert accession values to NCBI UIDs.

Get annotation package name from chip name

Defunct Functions in Package annotate

List GO Identifiers by GO Ontology

Run a blast query to NCBI for either a string or an entrez gene ID and then return a series of MultipleAlignment objects.

A function to generate an instantiation of a chromLocation class

A function to generate an instantiation of a pubMedAbst class

Returns a list of chromosome locations from a MAP environment

Class chromLocation, a class for describing genes and their chromosome mappings.

function to check to see if the packages represented by the names passed have the same version number

Drop GO labels for specified Evidence Codes

Create a Query String for an Entrez Gene Identifier

Create a Query String for Entrez Genes

Filter GO terms by a specified GO ontology

A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID

A function to open the browser to Genbank with the selected gene.

Get annotation map

Get the Evidence codes for a set of GO terms.

Functions to Access GO data.

Get GO terms for a specified ontology

extract publication details and abstract from annotate::pubmed function output

Functions to deal with Data Packages

Queries the NCBI database to obtain the sequence for a given GenBank Accession number

Functions to create hypertext links that can be placed in a table cell of a HTML file

Check for GO annotation

A dataset to show the human genome base pair locations per chromosome.

A dataset which contains the lengths (in base pairs) of the human chromosomes.

chromLocation instance hgu95AProbLocs, an example of a chromLocation object

Annotation data for the Affymetrix HGU95A GeneChip

Annotation data for the Affymetrix HGU95A GeneChip

Annotation data for the Affymetrix HGU95A GeneChip

Annotation data for the Affymetrix HGU95A GeneChip

Class "homoData"

Functions to build HTML pages

Get or verify valid IDs for a package or OrgDb object.

A Function To Generate HTML Anchors

Functions to map to organism IDs used by NCBI homology.

Convenience function for getting the organism from an object or package

A function to map from probes to unique Entrez Gene IDs

An interface to grep for PubMed abstracts.

Obtain the abstracts for a set PubMed list.

Obtain the titles of the PubMed abstracts.

HTML Generation for PubMed Abstracts

use web to populate MIAME instance with pubmed details

A function to query PubMed

Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.

A function to open the browser to Pubmed with the selected gene.

Function to extract data from the GEO web site

A Function To Serialize Environment

Functions to add arbitrary repositories

Take a list of symbols and translate them into the best possible ID for a package.

A function to select used genes on a chromosome from an ExpressionSet.