##GEM software suite
This software suite contains several methods for analyzing transcription factor binding and motif using genomic data (GEM, GPS, KMAC, KSM, RMD, etc.) and for discovering chromatin interactions (CID).
The complied Java software can be downloaded from http://groups.csail.mit.edu/cgs/gem/versions.html.
The orignal research papers can be found on the web pages of the individual tools.
##GEM
High resolution TF peak calling and motif discovery for ChIP-seq and ChIP-exo data, Genome wide Event finding and Motif discovery
http://groups.csail.mit.edu/cgs/gem/
##KSM and KMAC
KSM: a novel motif representation for transcription factor binding, K-mer Set Memory
KMAC: de novo motif discovery method, K-Mer Alignment and Clustering
http://groups.csail.mit.edu/cgs/gem/kmac/
##CID
Chromatin Interactoin Discovery for ChIA-PET and HiChIP data
http://groups.csail.mit.edu/cgs/gem/cid/
##RMD
Regulatory Module Discovery. Discovery of transcription factor co-binding patterns.
http://groups.csail.mit.edu/cgs/gem/rmd/
Developed by Yuchun Guo and the Gifford lab at MIT.