PySCUBA

Python for Single-cell Clustering Using Bifurcation Analysis.

Here be dragons!

This is still work in progress.

I have been tasked with redesigning into a Python package the Matlab code supporting the analysis presented in the following paper: Marco E, Karp RL, Guo G, Robson P, Hart AH, Trippa L, Yuan GC. (2014) "Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape". Proceedings of the National Acacdemy of Sciences, 111, E5643-E5650.

The motivation for this project is twofold:

• to make do without high Matlab licensing fees that were preventing some of our colleagues from using SCUBA and other tools developed at our lab;
• to come up with faster, more efficient way of handling the computations and data processing; a benchmark comparison done on the same machine and on a few datasets found that where SCUBA took about 20 minutes to complete, PySCUBA handles the same task in about 30 seconds.

I have found a few bugs, mathematical inconsistencies and improper or overlooked handling of outlier cases in the Matlab code. Such issues are fully addressed in the present Python package.

Reference

Marco E, Karp RL, Guo G, Robson P, Hart AH, Trippa L, Yuan GC. (2014) "Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape". Proceedings of the National Acacdemy of Sciences, 111, E5643-E5650.