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MICC: an R package for identifying chromatin interactions from ChIA-PET data.

ABSTRACT:

Unlabelled

ChIA-PET is rapidly emerging as an important experimental approach to detect chromatin long-range interactions at high resolution. Here, we present Model based Interaction Calling from ChIA-PET data (MICC), an easy-to-use R package to detect chromatin interactions from ChIA-PET sequencing data. By applying a Bayesian mixture model to systematically remove random ligation and random collision noise, MICC could identify chromatin interactions with a significantly higher sensitivity than existing methods at the same false discovery rate.

Availability and implementation

http://bioinfo.au.tsinghua.edu.cn/member/xwwang/MICCusage

Contact

michael.zhang@utdallas.edu or xwwang@tsinghua.edu.cn.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: He C

PROVIDER: S-EPMC4653385 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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Publications

MICC: an R package for identifying chromatin interactions from ChIA-PET data.

He Chao C Zhang Michael Q MQ Wang Xiaowo X

Bioinformatics (Oxford, England) 20150731 23

<h4>Unlabelled</h4>ChIA-PET is rapidly emerging as an important experimental approach to detect chromatin long-range interactions at high resolution. Here, we present Model based Interaction Calling from ChIA-PET data (MICC), an easy-to-use R package to detect chromatin interactions from ChIA-PET sequencing data. By applying a Bayesian mixture model to systematically remove random ligation and random collision noise, MICC could identify chromatin interactions with a significantly higher sensitiv ...[more]

PMID: 26231426

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