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
cosmoDAdirectory contains the python code to run the cosmoDA or genscore models. - The
srcdirectory contains the C code from genscore, as well as its extension from the cosmoDA model. - The
simulationandapplicationsdirectories contain the simulated and real data applications from the paper, respectively. - The
miscdirectory contains code for supplementary and concept figures. - The
figuresdirectory contains all generated figures.
1 maintainer
Metadata
1 maintainer
Release files for cosmoDA 0.1.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| cosmoda-0.1.0.tar.gz | 16.9 MB | Without provenance | Details for cosmoda-0.1.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| cosmoda-0.1.0-py3-none-any.whl | Python 3 | none | any | Details for cosmoda-0.1.0-py3-none-any.whl |
Total release size: 16.9 MB
Release files / cosmoda-0.1.0.tar.gz
| Download URL | cosmoda-0.1.0.tar.gz |
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| Tags | Python 3 |
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