scsketch 0.0.3

Interactive exploration of single-cell embeddings with directional analysis

scSketch

Interactive tooling for exploring single-cell embeddings in Jupyter (built on top of jupyter-scatter + anywidget).

Install (Pip)

If you already have JupyterLab installed, this is all you need:

pip install scsketch

If you do not have JupyterLab yet, install it (or use the convenience extra):

pip install jupyterlab
# or: pip install "scsketch[lab]"

Run

• Launch JupyterLab: jupyter lab
• Open demo.ipynb for an end-to-end example (it downloads example data from the internet).

Install (Conda / Fallback)

If pip install fails on your system (common with scientific packages), use conda:

git clone https://github.com/colabobio/scsketch.git
cd scsketch

conda env create -f environment.yml
conda activate scsketch

jupyter lab demo.ipynb

Troubleshooting

• Widgets don’t show up in JupyterLab:
  • Make sure ipywidgets and jupyterlab_widgets are installed in the same environment as jupyter lab.
  • Restart JupyterLab after installing dependencies.
  • If you’re on JupyterLab 3, you may need to run jupyter lab build once.

Development

With uv:

uv run jupyter lab demo.ipynb

Or with editable installs:

python -m venv .venv
source .venv/bin/activate
python -m pip install -e ".[dev]"
jupyter lab demo.ipynb