scAGN: Attention-based Graph Neural Network for Label Propagation in Single-Cell Omics

Requirements

• Ubuntu 18.04 LTS or higher
• Python 3.7.5
• R version 4.1.3

Installation

We will use Python 3.7.5. First create a python virtual environment.

conda create -n gcn python=3.7.5

Pytorch Installation

conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch

Pytorch-Geometric Installation

conda install pyg -c pyg -c conda-forge
pip install python-igraph
pip install umap-learn
pip install umap-learn[plot]

Preparation before running the code

1. Clone this repository in your home director

cd ~
git clone https://github.com/phycomlab/scAGN
# Create a folder to save intermediate outputs
mkdir gene-cn-output  

# cd ~/scAGN/data
# create folder for saving graph representation
# ./create_dir.sh

2. Download dataset. Dataset needs to be download to ~/scAGN/RScript/scData

cd  ~/scAGN/RScript/scData
wget <add-url>
./create_dir.sh

2. Generate CCA graph

cd scAGN/RScript/
./graph_generation.sh

3. Run scAGN on GSE108989

cd ~
~/scAGN/python/graph_AGN.py -i 128 -l 5 -d 0.0 -t 0.05 -r 0.1 -w 0.0000 -s 10 -G 0.8 -D GSE108989 -P 2000 > ~/scAGN/script/GRAPH_agn_4_GSE108989.txt

4. Run baseline methods

cd ~/scAGN/RScript
./do_CHETAH_prediction.sh
./do_scMap_prediction.sh
./do_seurat_prediction.sh
./do_singleR_prediction.sh

5. Generate plots used in the paper

cd ~/scAGN/python
python analysis.py

Licensing

License: MIT License 
Copyright Rahul Bhadani, Lingling An
Initial Date: Apr 16, 2022
Permission is hereby granted, free of charge, to any person obtaining 
a copy of this software and associated documentation files 
(the "Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to 
permit persons to whom the Software is furnished to do so, subject 
to the following conditions:

The above copyright notice and this permission notice shall be 
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF 
ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED 
TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A 
PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT 
SHALL THE AUTHORS, COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF 
CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF 
OR IN CONNECTION WITH THE SOFTWARE OR THE USE 
OR OTHER DEALINGS IN THE SOFTWARE.