listMarts

mart object created with the useMart function.  This is optional, as you usually use listMarts to see which marts there are to connect to.

mart

host to connect to if different then www.biomart.org

host

path to martservice that should be pasted behind the host to get to web service URL

path

port

boolean to indicate if function should return host of the BioMart databases

includeHosts

Boolean to indicate if you want to access archived versions of BioMart database

ssl.verifypeer

Give detailed output of what the method is doing, for debugging purposes

verbose

This function returns a list of BioMart databases to which biomaRt can connect to.  By default all public BioMart databases are displayed.  To establish a connection use the useMart function.

methods

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis.  biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.

listMarts: lists the avilable BioMart databases

Description

Usage

Arguments

Examples