Model based Interaction Calling from ChIA-PET data

This R package provides methods to detect chromatin interactions from ChIA-PET data.


Chao He, Michael Q. Zhang* and Xiaowo Wang*


Chao He <hechaobnu at gmail.com>


MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China.


Q: How to install MICC?

 In linux, type: R CMD INSTALL MICC_1.0.tar.gz. Do not forget to install R package VGAM at first.

Q: What is the input file of MICC?

 It is the raw PET clusters from ChIA-PET data, normally with 9 columns:

chr.   start   end   chr.   start   end   PET-count   total-PET-count-of-anchor-A   total-PET-count-of-anchor-B

For example: chr1   10000   12000   chr1   50000   53000   7   20   30

Q: How to get PET clusters from ChIA-PET sequencing data?

 By our MICCPERL scripts or any other ways you like.


Comments, suggestions, questions, bug reports, etc, are all welcome. For enquiries, please send emails to hechaobnu at gmail.com.


If you use the package, please cite us in the following way: 

Chao He, Michael Q. Zhang* and Xiaowo Wang*, MICC: an R package for identifying chromatin interactions from ChIA-PET data.

Anyone can use the source codes and executable files of MICC free of charge for non-commercial use.