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Quantifying 3D chromatin conformation stability

License: GNU General Public License v3.0

Python 16.64% Shell 1.44% R 42.09% Perl 7.92% Jupyter Notebook 31.91%

liquid-chromatin-hi-c's Introduction

Liquid-Chromatin-Hi-C

All code developed for the analysis of Liquid-Chromatin Hi-C assays.

A majority of code performs downstream analysis of Hi-C interaction matrices in cworld compatible HDF5 format:

with ongoing devlopment for compatibility with cooler format:

https://github.com/mirnylab/cooler

Usage Examples

Calculating Loss of Structure (LOS)

# Scale control Hi-C matrix and predigested Hi-C matrix
src/liquid_chromatin_HiC/scale.py -i control.hdf5
src/liquid_chromatin_HiC/scale.py -i predigest.hdf5

# Calculate 6 Mb cis percentage for scaled matrices
src/liquid_chromatin_HiC/hdf2RangeCisPercent.py -i control_scaleBy_x.hdf5
src/liquid_chromatin_HiC/hdf2RangeCisPercent.py -i predigest_scaleBy_x.hdf5

# Calculate LOS from cis percent bedGraphs
src/scripts/LOS.R -i predigest_cispercent.bedGraph -m control_cispercent.bedGraph

Calculating t_1/2

# With all *LOS.bedGraphs from multiple timepoints in directory
src/scripts/make_LOS_table.R
# With output LOS table of all timepoints
src/scripts/get_half_life_exponential.R -i LOS_40kb.txt -f True

Contributing to liquid-chromatin-Hi-C

All contributions, bug reports, bug fixes, documentation improvements, enhancements, and ideas are welcome!

References

Houda Belaghzal*, Tyler Borrman*, Andrew D. Stephens, Denis L. Lafontaine, Sergey V. Venev, Zhiping Weng, John F. Marko, Job Dekker. (2019). Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C. bioRxiv