README.md

In jeffbhasin/snpscope: snpscope: Compute overlap of SNPs with regulatory elements and export to CSV or the UCSC Genome Browser

snpscope

• Computes overlap of SNPs with regulatory elements and exports to CSV or the UCSC Genome Browser

• Uses shiny to launch a web-based user interface. This interface allows either a CSV download or the creation of a UCSC Genome Browser session via the rtracklayer package.

Installation

library(devtools)
options(repos=c("http://cran.rstudio.com","http://www.bioconductor.org/packages/release/bioc"))
install_github("snpscope", username="bluecranium")

Running

library(snpscope)
runWebApp()

Notes

• Adding custom tracks from BED files and CSV Download of overlaps do not work from within the package yet

• Need to implement a file chooser so the path to the BED files can be set from the interface

jeffbhasin/snpscope documentation built on May 19, 2019, 1:48 a.m.