https://github.com/open2c/looplib

A library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.
https://github.com/open2c/looplib

Last synced: 4 months ago
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A library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.

• Host: GitHub
• URL: https://github.com/open2c/looplib
• Owner: open2c
• Created: 2016-01-17T00:16:31.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2025-02-10T03:05:56.000Z (over 1 year ago)
• Last Synced: 2025-10-06T14:55:03.009Z (8 months ago)
• Language: Cython
• Size: 1.02 MB
• Stars: 10
• Watchers: 5
• Forks: 7
• Open Issues: 6
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

          
## 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