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:
# 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# 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 TrueAll contributions, bug reports, bug fixes, documentation improvements, enhancements, and ideas are welcome!
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