Installation

Stable release (recommended)

pip install sctrial

Optional dependencies

# plotting + GSEA
pip install "sctrial[plots,gsea]"

# AUCell scoring (pySCENIC)
pip install "sctrial[aucell]"

# survival analysis (lifelines)
pip install "sctrial[survival]"

# Bayesian DiD (PyMC)
pip install "sctrial[bayes]"

From source

git clone https://github.com/TheOmarLab/sctrial.git
cd sctrial
pip install .

Development setup

pip install -e ".[dev,plots,gsea,aucell,survival,bayes]"
pre-commit install

Notes

• Python: 3.9+ recommended.

• Runtimes: CPU‑only is sufficient for most workflows.

• GSEA: requires network access to fetch gene set libraries (or provide local GMT files).