Codes for 'Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue'

Resources

Patient's Compartment, TADs and Loops (reference genome hg19)

HiC-Pro 20k Matrices: resource folder (Links in Resource Readme)

Compartments: resource folder (pcori.bedGraph)

TADs: https://github.com/KunFang93/GISTA/tree/main/data

Loops: resource folder (Links in Resource Readme)

GISTA (Group, Individual-specific TADs Analyzer)

GISTA has its own github page https://github.com/KunFang93/GISTA

Single cell dataset

GSE240112

Citations

Paper is now published in Cell Report. If it helps your research, please consider cite it:

     Choppavarapu, L., Fang, K., Liu, T., Ohihoin, A. G., & Jin, V. X. (2025). Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue. Cell reports, 44(4).

Contact Us

Kun Fang: kf2799@cumc.columbia.edu; Victor Jin: vjin@mcw.edu