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Detect all superbubbles in a graph.

Project description

Linear Superbubble Detector


This project gives the reference implementation of the Linear Superbubble Dector (LSD).


  • Detect superbubbles in linear time
  • Uses NetworkX as graph library
  • Can load plenty file formats (everything that NetworkX can load )
  • Have different ways to report the superbubbles
  • Simple and clean code
  • Simple to understand and reimplement


The documentation can be found at:


The simples way to install is using pip:

pip install LSD-Bubble

You can also download the source from and run the make script to install the package. These needs that setuptools are installed.


The programms needs only a path to a graph file to work:

lsd path

If as input format not edgelist is used give the format with the -f parameter

lsd path -f gml

If you want a different reporting format use -r

lsd path -r count

If you want not to detect superbubbles but week superbubbles use –week:

lsd path –week

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Filename, size & hash SHA256 hash help File type Python version Upload date
LSD_Bubble-1.0-py3.6.egg (26.6 kB) Copy SHA256 hash SHA256 Egg 3.6
LSD_Bubble-1.0-py3-none-any.whl (13.2 kB) Copy SHA256 hash SHA256 Wheel py3
LSD-Bubble-1.0.tar.gz (8.4 kB) Copy SHA256 hash SHA256 Source None

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