MDM (formerly MCDIST)

 Bullet PURPOSE: R package MDM (formerly MCDIST) provides functions for the analysis of chromatin interactions using MC_DIST model (for one sample problem, i.e., detecting chromatin interactions from noises), Two-Step model and One-Step model (for two-sample problem, i.e., detecting differential chromatin interactions), based on Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) data.

The source package may be downloaded from the links below and can be installed on UNIX and Mac OS. In order to compile and install it, GNU Scientific Library (GSL) must be installed in advance.

 Bullet Software (source package; a .tar.gz file)

 Bullet Instructions for installing and runing MDM.

 Bullet Complete Manual (pdf file)

 Bullet Simulation code (with TFBS and TSS information needed in the simulation)

 Bullet References:

 Bullet If you have any questions, please email Liang Niu at or Shili Lin at