Helper functions and demonstration notebooks for iterative proximity ligation for
"From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging" Alexander A Boulgakov, Erhu Xiong, Sanchita Bhadra, Andrew D Ellington, Edward M Marcotte
https://doi.org/10.1101/470211
mycelium.py is a library of various helper functions.
R_spring_layout_demo.ipynb simulates layout of letter "R". See the top of each notebook input cell for step-by-step annotations. You can change which letter you want to layout near the top of the notebook as indicated. Such notebooks for each letter were used to create Fig. 4 & 6, and Supplementary Figs 3 & 4.
100_replicates_demo.ipynb simulates graph connectivity under various ligation regimes. This was used for Fig 5.