Scripts to simplify the annotation of .bed formatted files containing peaks or genomic regions.
See each directory's README file for descriptions of each script.
These scripts are designed for easy usage with GNU find, when you have a lot of .bed files that you want to annotate at once. For example:
find /path/to/peaks_dir -name "*.bed" ! -path "*/dir_I_dont_like/*" | xargs ./annotate.R