Piaso MCP server
io.github.genecell/piaso-mcp·v0.1.1·2 starsPIASO single-cell ecosystem docs (PIASO, COSG, cytome, LARIS, cytorete) + live PIASOmarkerDB
2 stars37 downloads/wk
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If you have run it, two minutes of your experience saves the next person an afternoon.
Piaso tools (12)
write = sends, deletes, buys or postsRead from the package source without running it. The installed server may list more.
check_versionsCurrent 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_implementationsCOSG (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_apiData-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_datasetOne PIASO-data registry entry (live): title, url, md5, size, cells, features, counts layer, reference, tutorials that use it.
get_markersAlias of query_marker_db (mirrors piaso.tl.getMarkers).
list_datasetsPIASO-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_studiesList the studies available in PIASOmarkerDB (proxies the live API; 36 at last check).
list_tutorialsThe 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_dbQuery the live PIASOmarkerDB for cell-type marker genes (proxies the piaso.org REST API).
resolve_installThe 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_docsSearch the PIASO ecosystem knowledge pack (works with zero packages installed).
version_matrixThe 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
- 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
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
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.
Alternatives to Piaso
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Context7Up-to-date docs for AI agentsnot reviewedWidely usedA- Svelte MCPThe official Svelte MCP server providing docs and autofixing tools for Svelte developmentnot reviewedWidely usedA
SvGridChecks AI-written SvGrid code against the real API, plus version-pinned Svelte 5 grid docs.not reviewedEstablishedA- Coolify46 optimized tools for managing Coolify infrastructure, diagnostics, and docs searchnot reviewedEstablishedB