README.md

In eonurk/bedtohomeR: Bed to Homer on Mac

bedtohomeR

An R package to convert bed formated files into Homer Ready txt format on Mac.

Installation:

library(dplyr) # install.packages("dplyr")
library(devtools) # install.packages("devtools")

then,

install_github("eonurk/bedtohomeR")

Usage

bed_to_homer(bed, "path/to/homer_ready_file.txt")

this will create a file with uniqueIDs and add "." for strands.

Then, you can go to terminal and use this file:

annotatePeaks.pl path/to/homer_ready_file.txt <genome> > output.txt

For more information: Homer Manual

License

This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3

eonurk/bedtohomeR documentation built on Jan. 1, 2020, 1:03 p.m.