Installation

Using pip

pip install scparadise -U

Create environment for using scparadise

conda create -n scparadise python=3.10

conda activate scparadise

pip install scparadise -U

If you want to use scParadise from R, you need to configure a Python environment in RStudio: Tools - Global Options - Python

Create environment from scparadise.yml (recommended)

1. Download scparadise_3.10.yaml or scparadise_3.11.yaml.

2. Install g++ (optional, for a clean installation):

sudo apt update
sudo apt-get install g++

3. Execute the following command in Anaconda (from directory with scparadise_3.10.yaml or scparadise_3.11.yaml):

conda env create -f scparadise_3.10.yaml

The installed environment is based on Python 3.10 (scparadise_3.10) or 3.11 (scparadise_3.11) and includes the latest version of scparadise, scvi-tools, scanpy, muon, harmony, jupyterlab, liana, decoupler and other packages for scRNA-seq analysis.

GPU support

scParadise automatically uses an NVIDIA GPU if available. If you do not have a GPU, scParadise will fall back to the CPU. We recommend using GPUs to train custom models, as training on CPUs can take a long time.