Installation

Using pip

pip install scparadise -U

Create environment for using scparadise in R

conda create -n scparadise python=3.9

conda activate scparadise

pip install scparadise -U

Set Python environment in R Studio: Tools - Global Options - Python

Create environment from scparadise.yml (recommended)

1. Download scparadise.yml.

2. Install g++ (optional, if you are doing a clean install):

sudo apt update
sudo apt-get install g++

3. Execute the following command in Anaconda (from directory with scparadise.yml):

conda env create -f scparadise.yml

Installed environment includes latest scparadise, scvi-tools, scanpy, muon, harmony, jupyterlab and other packages for scRNA-seq analysis.

GPU support

scParadise supports GPU (NVIDIA) usage automatically. If you don’t have GPU scParadise will automatically use CPU. We recommend using GPUs to train custom models as training on CPUs can take a long time.