scSHARP Installation


For further installation information visit our Github repositories for the scSHARP tool and R tools

Also see our distribution on pypi


scSHARP and its dependencies can be installed in a few simple steps:

R package installation

Our package utilizes a suite of cutting edge single cell classification tools which we have compiled as an R package. Please install by following instructions here.

Note: the R tools are necessary for running scSHARP

Create a conda environment:

conda create -n <env name> python=3.9

conda activate <env name>

scSHARP package install

Installing with Pip:

Install with Pip if you plan on running R4scSHARP from Python.

pip install scSHARP

conda install pytorch-cluster -c pyg

Installing with conda

Install with Conda if you do not plan on running R4scSHARP from Python.

conda install -c lewinsohndp scsharp -c pyg -c conda-forge -c r