🧬 Single-cell Cytometry Annotation Network
Based on biological knowledge prior, Scyan provides a fast cell population annotation without requiring any training label. It is an interpretable model that also corrects batch-effect and can be used for debarcoding, cell sampling, and population discovery.
Documentation
The complete documentation can be found here. It contains installation guidelines, tutorials, a description of the API, etc.
Overview
Scyan is a Bayesian probabilistic model composed of a deep invertible neural network called a normalizing flow (the function $f_{\phi}$). It maps a latent distribution of cell expressions into the empirical distribution of cell expressions. This cell distribution is a mixture of gaussian-like distributions representing the sum of a cell-specific and a population-specific term. Also, interpretability and batch effect correction are based on the model latent space — more details in the article's Methods section.
Getting started
Installation
Scyan can be installed on every OS with pip for python>=3.11:
pip install scyan
Basic usage / Demo
import scyan
adata, table = scyan.data.load("aml") # Automatic loading
model = scyan.Scyan(adata, table)
model.fit()
model.predict()
This code should run in approximately 40 seconds (once the dataset is loaded). For more usage demo, read the tutorials or the complete documentation.
Cite us
Our paper is published in Briefings in Bioinformatics and is available here.
@article{10.1093/bib/bbad260,
author = {Blampey, Quentin and Bercovici, Nadège and Dutertre, Charles-Antoine and Pic, Isabelle and Ribeiro, Joana Mourato and André, Fabrice and Cournède, Paul-Henry},
title = "{A biology-driven deep generative model for cell-type annotation in cytometry}",
journal = {Briefings in Bioinformatics},
pages = {bbad260},
year = {2023},
month = {07},
issn = {1477-4054},
doi = {10.1093/bib/bbad260},
url = {https://doi.org/10.1093/bib/bbad260},
eprint = {https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad260/50973199/bbad260.pdf},
}
1 maintainer
Metadata
1 maintainer
Release files for scyan 1.8.0
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|---|---|---|---|---|
| scyan-1.8.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 120.9 kB
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