/GenKI

Primary LanguagePythonMIT LicenseMIT

GenKI (Gene Knock-out Inference)

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

drawing


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 (from source)

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

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

Usages

Quick Start