CryptFusion

This Jupyter Notebook is an accompaniment to the paper 'Crypt fusion as a homeostatic mechanism in the human colon' by Baker A-M, Gabbutt C, Williams M, Cereser B, Jawad N, Rodriguez-Justo M, Jansen M , Barnes CP, Simons BD, McDonald S, Graham TA, Wright NA. Gut doi:10.1136/gutjnl-2018-317540. In this paper, we use clonal lineage trancing techniques to provide the first evidence of crypt fusion in the human colon. Further, we explore the effects crypt fusion on the distribution of patch sizes (where a patch is defined as a cluster of neighbouring clonally related crypts) and provide an updated estimate of the crypt fission rate (0.011 divisions per crypt per year) which is approximately 20% higher than estimates excluding fusion. We combine the number of observed bifurcations with the calculated crypt fission rate to estimate the duration of crypt fission In this notebook, we present all the code used to generate these results.