Code to reproduce the figures and results in the preprint "Analytical solutions of the chemical master equation with bursty production and isomerization reactions" by Gennady Gorin and Lior Pachter.
dag_cme_burst.py implements the DAG generation, stochastic matrix construction, simulation, and analytical solution routines.
gg211028_dag_2.ipynb demonstrates that the algorithm concords with simulations, and benchmarks the algorithm's runtime.
gg211030_fltseq_5.ipynb applies the algorithm to an FLT-seq long-read sequencing dataset and validates the consistency of theoretical correlation constraints on inter-gene and intra-gene correlation matrices.