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PIASO

Precise Integrative Analysis of Single-cell Omics

PIASO is a Python toolkit for single-cell omics analysis: marker-gene-guided dimensionality reduction (GDR), INFOG normalization, gene-set scoring, cell-type annotation and label transfer, and a plotting suite built for publication figures.

It works on an AnnData in memory, and on cytome datasets by streaming from disk in chunks — peak memory is set by the batch size rather than by the number of cells, so the same functions run on a few thousand cells or on several million.

Documentation

piaso.org

Installation

Install from PyPI (stable release):

pip install piaso-tools

This also installs cytome, the on-disk dataset format PIASO reads and writes. Nothing extra to install to work with .cytome files.

Install from bioconda (stable release):

conda install -c conda-forge -c bioconda piaso

Install from GitHub (latest development version):

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

Using PIASO with a coding agent

PIASO-for-agents makes the PIASO ecosystem available to coding agents from one canonical knowledge base, generating Claude skills, Cursor rules, AGENTS.md, llms.txt, and an MCP server. Useful if you work in Claude Code, Cursor, Copilot, Codex, Windsurf, Cline, or Aider and want the agent to know the current API rather than guess it.

Citation

If PIASO is useful for your research, please consider citing Wu, S.J., Dai, M. et al. Pyramidal neurons proportionately alter cortical interneuron subtypes. Nature (2026). https://doi.org/10.1038/s41586-025-09996-8

Contact

Min Dai dai@broadinstitute.org

Project links

Data verified by PyPI on Aug 16, 2026
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Credits

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Author: Min Dai

Maintainer: Min Dai

GitHub Statistics

Data verified by PyPI on Aug 16, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

BSD-3-Clause

Requires

Python >=3.9

Provides Extra

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