/looplib

A library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.

Primary LanguageCython

Simulate loop extrusion by loop extruding factors and analyse the resulting structures of loops.

  • simlef.pyx - simulate loop extrusion in 1d with simulate()

  • looptools.py - analyse the structure of extruded loops:

    • build trees of nested loops with get_parent_loops()
    • find root loops with get_roots()
    • identify the positions between the root loops with get_backbone()
    • identify stacked LEFs with stack_lefs()

  • loopviz.py - visualize loops with plot_lefs()

  • simlef_twosided.pyx - simulate loops extrusion with synchronized extrusion blocking