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Getting started


scida can be installed via PyPI. scida requires a Python version 3.9, 3.10 or 3.11.

Encapsulating packages

We recommend encapsulating your python environments. For example using anaconda or virtualenv.

If you use anaconda, we recommend running

conda create -n scida python=3.9

Activate the environment as needed (as for the following installation) as

conda activate scida

If you are using jupyter/ipython, install and register the scida kernel via

conda install ipykernel
python -m ipykernel install --user --name scida --display-name "scida"

Now you can install scida as described below and use it in jupyter notebooks with the given kernel.

pip install scida

Next steps

Next, get started with the tutorial for either simulations or observations:


Tutorial on a simulation dataset.


Tutorial on an observational dataset.