Software (source package; a .tar.gz file)
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.
Software (source package; a .tar.gz file)
Instructions
for installing and runing MDM.
Complete Manual
(pdf file)
Simulation code (with TFBS and TSS information needed in the simulation)
References:
Liang Niu and Shili Lin, Statistical Models for Detecting Differential Chromatin Interactions Mediated by a Protein, submitted.
If you have any questions, please email Liang Niu at niu.13@osu.edu
or Shili Lin at shili@stat.osu.edu.