the Monod package fits CME models to sequencing data.

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Monod: a package for CME inference from seq data

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This repository contains the current version of the Monod package, which implements procedures for fitting and analyzing stochastic models of transcription and sequencing. The description of the package's functionality and several applications are given in the preprint.

Examples and tutorials are given at the example repository. For theoretical background, see Gorin & Pachter 2022. For usage instructions, see the readthedocs website. For a sample workflow applied a small dataset, see the Colaboratory notebook.

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