Contains jupyter notebooks analysing single cell Hi-C structures. Relies on NucFrames code.
The file loop_analysis.ipynb performs monte carlo analysis of CTCF/Cohesin loops. This code aims to detect whether loop anchor points, detected by Rao et al., are seen to interact in 3d space, across our single cell Hi-C structures, more frequently than randomly selected points with the same sequence separation.
Requires python3. Using Anaconda to create a fresh environment, and then manage these requirements, is suggested. All packages can be installed with pip or conda.
- Seaborn
- pyliftover
- jupyter
Run jupyter notebook in the cloned folder. A web browser should open. View
loop_analysis.ipynb to view and run the analysis.
The .hdf5 files required to run these scripts are availiable from GEO,
accession number GSE80280. These files must be downloaded prior to running these
scripts.
Additionally, a file defining loop locations is required (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525). This file was generated by Rao et al..