ucscGenomes: Get available genomes on UCSC

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

Description

Get a data.frame describing the available UCSC genomes.

Usage

ucscGenomes(organism=FALSE)

Arguments

organism

A logical(1) indicating whether scientific name should be appended.

Details

For populating the organism column, the web url http://genome.ucsc.edu/cgi-bin is scraped for every assembly version to get the scientific name.

Value

A data.frame with the following columns:

db	UCSC DB identifier (e.g. "hg18")
species	The name of the species (e.g. "Human")
date	The date the genome was built
name	The official name of the genome build
organism	The scientific name of the species (e.g. "Homo sapiens")

Author(s)

Michael Lawrence

See Also

UCSCSession for details on specifying the genome.

Examples

ucscGenomes()

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.