Our Packages

We have developed the following open-source software packages to analyze high-throughput genomics data with biophysical models. Click on the cards to explore our tools!

Monod

Monod: CME inference from seq data

biVI

biVI: Biophysical modeling with variational autoencoders

meK-Means

meK-means: Biophysically interpretable inference of cell types

Chronocell

Chronocell: Trajectory inference from single-cell data

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Generating unspliced and spliced count matrices with kallisto

Our tools require as inputs spliced and unspliced UMI counts per gene and per cell (two cell by gene matrices). The current version of our alignment software kallisto outputs these count matrices, as described in detail in the protocol preprint.

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