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

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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

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

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