diChIPMunk  motif discovery using dinucleotide PWMs

UPDATE! ChIPMunk and diChIPMunk in a single package!

diChIPMunk is now merged with ChIPMunk, please grab the last version at http://autosome.ru/ChIPMunk


diChIPMunk paper is now published:
IVAN KULAKOVSKIY et al, J. Bioinform. Comput. Biol. (2013) DOI: 10.1142/S0219720013400040 (c) [World Scientific Publishing Company];
postprint electronic version of the published article can be found here.


Actual release (March-April 2013): diChIPMunk binaries, diChIPMunk sources.
Examples: ChIP-Seq data used in diChIPMunk benchmark, resulting PWMs from di/mono ChIPMunks.
Supporting tools: DI-MACRO-APE, "lite" dinucleotide fork of MACRO-APE. Requires Ruby 1.9.
Previous versions: diChIPMunk binaries f0, diChIPMunk sources f0. diChIPMunk binaries f1, diChIPMunk sources f1.

Quick-start information

To use diChIPMunk you need Java Runtime Environment (JRE) >1.6 installed. Most modern Linux distributions have Java preinstalled or available in package repositories (still OpenJDK would be slightly slower than Oracle version). Windows users can directly download JRE here.

Note! diChIPMunk uses the same command-line format as the original ChIPMunk, see manual.
There are two important differences:
- diChIPMunk lives in the autosome.ru.di package so the command line should be changed accordingly: java autosome.ru.ChIPMunk should be changed to java autosome.ru.di.ChIPMunk ;
- diChIPMunk is able to use only 'uniform' and 'auto/local' background settings (no user-defined GC content % as for simple ChIPMunk).
As ChIPMunk for KDIC, diChIPMunk uses 1/N scaling koefficient for KDIDIC (omitted in KDIDIC definition, see paper).



Funding: This work was supported, in part, by a Dynasty Foundation Fellowship; Russian Foundation for Basic Research [12-04-32082-mol_a and 12-04-01736-a]; Program "Cell and Molecular Biology" of the Presidium of RAS.