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MIA-Sig

Introduction

MIA-Sig enables the analysis of multiplex chromatin interaction data by signal processing and statistical algorithms. It can

• remove doublets and triplets in droplet-based data
• assign statistical significance to each chromatin complex via distance test
• call topologically associating domains (TADs) directly on multiplex data
• identify subsets of TADs frequently in contact
• assess significance of protein-enriched complexes by the enrichment test

MIA-Sig has been tested on ChIA-Drop and RNAPII ChIA-Drop (Zheng et al., 2019) data, and can potentially be applied to GAM (Beagrie et al., 2017) and SPRITE (Quinodoz et al., 2018) data.

Get acquainted

• Read ChIA-Drop paper for experimental protocols:
  Multiplex chromatin interactions with single-molecule precision, Zheng et al., Nature, 2019

• Read ChIA-DropBox preprint for data processing and visualization:
  ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions, Tian et al., bioRxiv, 2019

• Read MIA-Sig paper for algorithmic details:
  MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms, Kim et al., Genome Biology, 2019

• Browse through MIA-Sig results:
  miasig_files Box Sync folder contains data and results presented in our preprint. Feel free to visualize results on Juicebox by downloading the .hic files.

Get started

1. Install dependencies.
2. Set up MIA-Sig.
3. Follow tutorials to run test datasets.

• ChIA-Drop data
• RNAPII ChIA-Drop data

4. Use MIA-Sig in your own projects.

Contact

Contact Minji (minji.kim@jax.org) for questions or comments.