wentaoStyle / GenKI

GenKI (Gene Knock-out Inference)

A VGAE (Variational Graph Auto-Encoder) based model to learn perturbation using scRNA-seq data.
Paper

Install dependencies

Fist install dependencies of GenKI with conda:

conda env create -f environment.yml
conda activate ogenki

Install pytorch-geometric following the document:
https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html

Install GenKI with pip:

pip install git+https://github.com/yjgeno/GenKI.git

or install it manually from source:

git clone https://github.com/yjgeno/GenKI.git
cd GenKI
pip install .

Tutorial

Virtual KO experiment:
https://github.com/yjgeno/GenKI/blob/master/notebook/Example.ipynb