BEP_CBIO

CODE

main.ipynb

In this file, the overlap function is called, the similarity matrix is computed and the HCS clustering is performed.

data_preprocessing.ipynb

In this file, the .bed files are converted to the csv file.

Overlap.py

This file contains the overlap algorithms. The n2_overlap() function is just the brute force method used in testing. The remaining functions are part of the sweep line algorithm.

Graph.py

Class to create a graph object.

HCS.py

Highly connected subgraph class.

DATA

region_data.csv and similarity_matrix.npy are to big for github

metadata.csv

The first line shows the tissues in the dataset (in correct order) The second line shows the amount of active regions in the tissues of line 1 The last line shows the chromosomes (and in which order) used in this work

overlap_matrix.npy

Amount of overlap between the tissues in a numpy matrix