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Introduction

scGen is a generative model to predict single-cell perturbation response across cell types, studies and species (Nature Methods, 2019). scGen is implemented using the scvi-tools framework.

Getting Started

What you can do with scGen:

import scanpy as sc

adata = sc.read(data)
sc.pp.normalize_total(adata)
sc.pp.log1p(adata)

Installation

Installation with pip

To install the latest version scGen via pip:

pip install scgen

or install the development version via pip:

pip install git+https://github.com/theislab/scgen.git

Examples

See examples at our documentation site.

Reproducing paper results

In order to reproduce paper results visit here.

References

Lotfollahi, Mohammad and Wolf, F. Alexander and Theis, Fabian J. "scGen predicts single-cell perturbation responses." Nature Methods, 2019. pdf