cosmoDA 0.1.0

Compositional Score Matching Optimization for Differential Abundance Testing

cosmoDA - Compositional Score Matching Optimization for Differential Abundance Testing

This repository contains the cosmoDA model (Ostner et al., 2024), as well as a Python interface to the score matching estimator for power interaction models in the genscore R package (Yu et al., 2024). It also contains all code needed to reproduce the analyses in the publication (TODO).

For usage info, please refer to the tutorial.

Raw and intermediate data objects can be downloaded on zenodo. Simply download the data directory from there and unpack it in the cosmoDA directory.

Installation

TODO

Usage

TODO

Repository structure

This repository is structured as follows:

• The cosmoDA directory contains the python code to run the cosmoDA or genscore models.
• The src directory contains the C code from genscore, as well as its extension from the cosmoDA model.
• The simulation and applications directories contain the simulated and real data applications from the paper, respectively.
• The misc directory contains code for supplementary and concept figures.
• The figures directory contains all generated figures.