Distinguishing biophysical stochasticity from technical noise in single-cell RNA sequencing usingMonod

Abstract

AbstractWe present the Python packageMonodfor the analysis of single-cell RNA sequencing count data through biophysical modeling.Monodnaturally “integrates” unspliced and spliced count matrices, and provides a route to identifying and studying differential expression patterns that do not cause changes in average gene expression. TheMonodframework is open-source and modular, and may be extended to more sophisticated models of variation and further experimental observables.TheMonodpackage can be installed from the command line using pip install monod. The source code is available and maintained athttps://github.com/pachterlab/monod. A separate repository, which contains sample data and Python notebooks for analysis withMonod, is accessible athttps://github.com/pachterlab/monod_examples/. Structured documentation and tutorials are hosted athttps://monod-examples.readthedocs.io/.