scSHARP

Repository for "Consensus Label Propagation with Graph Convolutional Networks for Single-Cell RNA Sequencing Cell Type Annotation" extended abstract submission for Learning on Graphs Conference and full paper available at https://doi.org/10.1101/2022.11.23.517739.

Installation (pypi)

Create a new conda environment

conda create -n <env name> python=3.9
conda activate <env name>

Install pip to conda environment

conda install pip

Install torch

Linux with GPU:

conda install pytorch pytorch-cuda=11.7 -c pytorch -c nvidia

Mac OS:

conda install pytorch -c pytorch

Install torch geometric

conda install pyg -c pyg

Install scSHARP

You will need to use the version of pip installed to your new conda environemt. In order to find the path to your conda environment, you can use:

conda config --show envs_dirs

Run the pip install of scSHARP directly from the binary in yout conda directory

./anaconda/envs/<env_name>/bin/pip install scSHARP

Installation of torch and torch geometric required prior to pip install.

See demo.ipynb for example work flow. Please input raw counts.