- Obtains data by direct downloading and updating of a local mirror of select UCSC Genome Browser annotation tables
- R package contains functions to assess genomic context of any given set of genomic ranges by performing overlaps with regions of annotated genomic features and produce long, short, and plot outputs
- Also contains a script that allows annotation of a flat file from the command line, without needing the user to code in R
- getUCSCTable has been implemented which supports downloading and loading of any UCSC table from any UCSC genome into R, and can optionally sync a local cache of these tables
From R:
library(devtools)
install_github("goldmine", user="bluecranium")
Example: Loading knownGene on the fly to a data.frame
library(goldmine)
knownGene <- getUCSCTable("knownGene","hg19")