# PIASO-for-agents

> Agent-neutral knowledge hub for the PIASO single-cell omics ecosystem (Gord Fishell Lab, HMS / Broad). One canonical source generates every agent format (Claude skill, Cursor rules, AGENTS.md, llms.txt, MCP).

## Components
- [piaso](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/components/piaso.md): python, install `pip install piaso-tools "matplotlib<3.9"`
- [cosg](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/components/cosg.md): python, install `pip install cosg`
- [cosgr](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/components/cosg.md): r, install `remotes::install_github("genecell/COSGR")` (documented with cosg)
- [laris](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/components/laris.md): python, install `pip install laris`
- [emergene](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/components/emergene.md): python, install `pip install emergene`

## Workflows
- [Workflow — end-to-end scRNA-seq (load → clusters → markers → GDR)](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/workflows/end_to_end_scrnaseq.md)
- [Workflow — ligand–receptor / cell–cell communication](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/workflows/ligand_receptor.md)
- [Workflow — marker-based cell-type annotation](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/workflows/marker_based_annotation.md)
- [Workflow — cell-type inference from PIASOmarkerDB](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/workflows/markerdb_annotation.md)

## Optional
- [gotchas](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/gotchas.md)
- [data fixtures](https://raw.githubusercontent.com/genecell/PIASO-for-agents/master/canonical/data.md)

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Maintained by **[The Fishell Laboratory](https://fishelllab.hms.harvard.edu)** (Harvard Medical School / Broad Institute).