Installation

pip install piaso-tools

The distribution is piaso-tools; the import is import piaso. Pre-compiled wheels ship for Linux, macOS (Intel and Apple Silicon) and Windows on Python 3.9–3.12, so there is nothing to build.

This also installs cytome, the on-disk dataset format PIASO reads and writes, and COSG for marker genes.

From bioconda

conda install -c conda-forge -c bioconda piaso

Development version

pip install git+https://github.com/genecell/PIASO.git

Optional extras

pip install 'piaso-tools[scanpy]'

scanpy is only needed for interoperability with scanpy-based workflows. The core workflow — normalization, dimensionality reduction, neighbours, clustering, UMAP, marker genes and plotting — runs without it.

An environment for the tutorials

The tutorials run on a plain PIASO install — there is no separate tutorial dependency set:

conda create -n piaso_env python=3.10 -y
conda activate piaso_env
pip install piaso-tools

python -c "import piaso; print(piaso.__version__)"

To run them as notebooks, register the environment as a Jupyter kernel:

pip install ipykernel
python -m ipykernel install --user --name piaso_env --display-name "Python (piaso_env)"

Two packages that similar guides ask for are not needed here:

often suggested	why not
pip install 'scanpy[leiden]'	piaso.tl.leiden clusters through igraph directly. PIASO has no scanpy dependency; pip install 'piaso-tools[scanpy]' exists only for interoperating with existing scanpy code.
pip install scrublet	piaso.pp.scrublet is PIASO’s own implementation of the algorithm, streaming and library-aware.

cytome comes with piaso-tools; the tutorials that stream from disk need nothing extra.