Epi-Speller v.0: a framework for searching and interpreting epigenomic signatures 

Epi-Speller is a program for analyzing multiple genome-wide profling epigenomic data. It includes:
- Signal discretization	based on automatic inference of cut-offs for genome-wide signal levels.
- Clustering based on letter-representation.
- Using sequence logo to summarize the frequent signals using Weblogo.

System requirements:
Linux-based, Mac OSX, g++ 4.7 or above, Perl 5.12.3, R 2.15 

Install, uninstall, configuration, and operating instructions.
g++ epi_letter.cpp -o epi_letter
other files are script files which does not need to install, just run.

Files list.
alphabet_chrom.R	- assigning epi-letter for genomic regions based on grouping algorithm
dictionary_maker.pl	- creating the list of epi-letters
epi_letter.cpp		- grouping algorithm to define the cutoffs for genome-wide level evaluation
epimotif_scanning.pl	- searching for patterns
hamming_distance.pl	- computing Hamming distance
try_clustering.R	- k-means clustering

Implemented by Huy Q. Dinh (CIBIV/MFPL) (contact email: huy.dinh@univie.ac.at)
12 Nov 2012