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Piaso MCP server

by genecell·io.github.genecell/piaso-mcp·v0.1.1·2 stars

PIASO single-cell ecosystem docs (PIASO, COSG, cytome, LARIS, cytorete) + live PIASOmarkerDB

A92/100grade A
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Safety scan
A92/100

full report

Adoption
Growing

2 stars37 downloads/wk

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Piaso tools (12)

write = sends, deletes, buys or posts

Read from the package source without running it. The installed server may list more.

  • check_versions

    Current PyPI release of each Python package vs the version this snapshot was tested against. Pure PyPI JSON (network); use it to disclose drift ('docs tested on 1.2.3, you have 1.3.0').

  • compare_implementations

    COSG (Python) vs COSGR (R) divergences — params, defaults, data-object contract — and, for 'cytome', the Python vs R cytome packages. This knowledge exists nowhere else.

  • get_api

    Data-object contract (reads/writes, defaults, what it computes) for a PIASO / COSG / cytome / LARIS / Emergene / cytorete function, from the component docs. The exact live signature is on the generated API reference at https://piaso.org/api/ (or `inspect.signature` after install).

  • get_dataset

    One PIASO-data registry entry (live): title, url, md5, size, cells, features, counts layer, reference, tutorials that use it.

  • get_markers

    Alias of query_marker_db (mirrors piaso.tl.getMarkers).

  • list_datasets

    PIASO-data datasets (live registry from genecell/PIASO-data, cached 24 h): id, format, size, species, cells, counts layer, how to load. Falls back to the bundled data.md offline.

  • list_studies

    List the studies available in PIASOmarkerDB (proxies the live API; 36 at last check).

  • list_tutorials

    The piaso.org tutorial index (executed, human-reviewed): title, URL, what it covers, which components it uses. Filter by topic (scRNA-seq, methods, marker-genes, annotation, gene-sets, spatial, grn, cell-cell-interaction, plotting-data) and/or component (piaso, cosg, cytome, laris, cytorete, emergene). Route the user to the tutorial for their platform before writing code.

  • query_marker_db

    Query the live PIASOmarkerDB for cell-type marker genes (proxies the piaso.org REST API).

  • resolve_install

    The exact install line(s) for a set of components in a given language (python|r), including extras. Answers 'I'm in R and want this chain — what do I install?' — the most error-prone thing in an independently-installed, cross-language ecosystem. Never suggests a matplotlib pin.

  • search_docs

    Search the PIASO ecosystem knowledge pack (works with zero packages installed).

  • version_matrix

    The component versions this knowledge pack was tested against (from meta.yaml), with install lines, roles and citations — so an agent can state what the docs assume.

Public scan report

scanner v0.1.10 · 2026-10-16 · same rubric, same numbers if you re-run it

no findings
  • Code scan6 source files scanned25/25
  • –Live reliabilityno gateway calls yet and no remote to proben/a
  • –Tool poisoningtools not inspected (local package is not executed); not countedn/a
  • Auth qualitylocal package, no credentials required12/15
  • Maintenancelast push 17 days ago15/15
  • Maintainer identityregistry namespace matches repository owner; GitHub account older than a year8/10
Overall 92/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

How Piaso compares

Against every graded Productivity MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score
92/100
higher than 90% of 1,301 Productivity servers
Tools
12
the typical Productivity server has 7
Tools that change things
0%
typical: 0%. Fewer write tools means less an agent can break
GitHub stars
2
more than 60% of 855 Productivity servers
Downloads a week
37
more than 23% of 433 Productivity servers with a package

What its tools let an agent do: 12 read

Release history: 2 versions in the registry since 2026-09-05, latest 2026-09-29, typically one every 24 days.

Install Piaso in Claude Code, Cursor or VS Code

claude mcp add piaso-mcp -- uvx piaso-mcp
Add to Cursor

What the publisher says

From the Piaso repository's README, as published. We do not edit it. Read it on GitHub

PIASO-for-agents

Make the PIASO single-cell omics ecosystem first-class for any coding agent — Claude Code, Cursor, Copilot, Codex, Windsurf, Cline, Aider — from one canonical, agent-neutral knowledge pack.

Maintained by The Fishell Laboratory (Harvard Medical School / Broad Institute). Every agent-specific format (Claude skill, Cursor rules, AGENTS.md, llms.txt, MCP server) is a generated artifact built from canonical/ — never a hand-maintained copy. A CI drift check (python build.py --check) fails the build if any dist/ artifact is out of sync with canonical/, and the code-block test suite runs every canonical block against the pinned component versions on every push, nightly, and on component releases, so the guidance cannot silently rot.

Hub v0.2.0 · piaso-mcp 0.1.0 — tested against piaso-tools 1.2.3 · cosg 1.2.0 · cytome 0.3.1 · laris 0.13.0 · emergene 1.0.2 · cytorete 0.1.1 · COSGR 1.0.0 · cytome (R) 0.1.0 (2026-09-04).

The ecosystem

Independently-installable packages under github.com/genecell, in four layers. Dependencies run one way (cytorete → piaso-tools → cosg + cytome; laris → cosg), and pip install piaso-tools already brings COSG and cytome.

Each component is independently installable — a COSG-only, cytome-only or LARIS-only user is a first-class citizen, and every canonical/components/.md assumes nothing else is installed. The hub's unique value is documenting how the components compose, and the cross-component choices no single repo can make: SCALAR vs LARIS (dissociated vs spatial ligand–receptor — same CellChatDB either way), AnnData vs .cytome (in memory vs streamed — same function calls), COSG vs cytorete (marker genes vs the TFs that drive them), Python vs R (COSG → COSGR, cytome → cytome (R); everything else via a .cytome handoff), and which annotation route** (marker sets, reference projection, joint embedding, or a gene list against PIASOmarkerDB).

Inside piaso-tools

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

Piaso: common questions

Is Piaso MCP server safe?
Yes, by our scan: it is graded A (92/100). Read the Piaso safety report
How do I install Piaso?
It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does Piaso need an API key?
Not as far as the registry entry and our scan can tell: no credentials are declared or required.
Is Piaso maintained?
The last commit was 38 days ago (2026-09-29). The latest release is v0.1.1.
What can I use instead of Piaso?
Servers from other publishers that do the same job: Livewire Flux MCP server, Context7 MCP server and Svelte MCP server.
How does Piaso compare with other Productivity MCP servers?
safety score 92/100 (higher than 90% of 1,301 Productivity servers); tools 12 (the typical Productivity server has 7); tools that change things 0% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.

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