Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell...

Single-cell RNA sequencing analysis centers on illuminating cell diversity and understanding the transcriptional mechanisms underlying cellular function. These datasets are large, noisy, and complex. Current analyses prioritize noise removal and dimensionality reduction to tackle these challenges and extract biological insight. We propose an alternative, physical approach to leverage the stochasticity, size, and multimodal nature of these data to explicitly distinguish their biological and technical facets while revealing the underlying regulatory processes. With the Python package Monod, we demonstrate how nascent and mature RNA counts, present in most published datasets, can be meaningfully "integrated" under biophysical models of transcription. By utilizing variation in these modalities, we can identify transcriptional modulation not discernible though changes in average gene expression, quantitatively compare mechanistic hypotheses of gene regulation, analyze transcriptional data from different technologies within a common framework, and minimize the use of opaque or distortive normalization and transformation techniques.