Installation

Requirements

• Python 3.10–3.13
• A Jupyter environment (JupyterLab 4+ recommended)

Basic installation

pip install sclab

With Scanpy (recommended)

Most workflows require Scanpy. Install it alongside SCLab:

pip install "sclab[scanpy]"

With JupyterLab

pip install "sclab[jupyter]"

All optional dependencies at once

pip install "sclab[scanpy,jupyter]"

Development installation (uv)

If you are working on SCLab itself, clone the repository and install with uv:

git clone https://github.com/umbibio/sclab.git
cd sclab
uv sync --all-groups

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Optional: R dependencies

Some features require R:

• Differential expression — pseudobulk_edger, pseudobulk_limma
• Imputation — ALRA

See the R Setup guide for instructions.

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Verify installation

import sclab
print(sclab.__version__)