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.
You will need one R dependency to run scSHARP. Repository and install instructions can be found here
conda create -n <env name> python=3.9
conda activate <env name>
conda install pip
Linux with GPU:
conda install pytorch pytorch-cuda=11.7 -c pytorch -c nvidia
Mac OS:
conda install pytorch -c pytorch
conda install pyg -c pyg
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.