io.github.genecell/piaso-mcp
PYPI · PIASO-MCP
PIASO single-cell ecosystem docs (PIASO, COSG, cytome, LARIS, cytorete) + live PIASOmarkerDB
Available components
Last scanned (17 hours ago)
Scores higher than 69% of PyPI servers
Category Health and Science
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security50
- Malware scan not yet available for this package.Unverified
- No known CVEs affecting this package version or its production dependencies.Pass
- Runs hatchling.build at install time, a recognised build step with no custom scripting around it. View diagnostics → Pass
- 1 of 29 dependencies flagged as unhealthy. View diagnostics → Partial
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to genecell/PIASO-for-agents). View diagnostics → Pass
- Clear OSI-approved license (BSD-3-Clause).Pass
- Actively maintained (last published 36 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability75
- AI-judged instruction clarity (good).Pass
- Tool/resource definitions use about 872 tokens (~72/item across 12 items; 12 tools + 0 resources), lean.Pass
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management67
- Stability observed for 20 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage71
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 0% of tool parameters carry a description.Fail
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 12 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 12 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 4 Nov 26 −5
- Stability: pass → 0.67 functional
- 29 Oct 26 −15
- Malware scan: pass → unverified ▼ security
- 27 Oct 26 +1
- Stability: 0.97 → pass security
- 25 Oct 26 −1
- Stability: pass → 0.93 functional
- 19 Oct 26 +1
- Stability: 0.97 → pass security
- 17 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 90 to 93. That category is still filling its 30-day observation window: 27 days of observed history at the previous scan, 28 at this one. The score rises as the window fills, whether or not the server changes.
- 15 Oct 26 +42
- Injection markers: unverified → pass ▲ security
- Tool coverage: unverified → 100 ▲ functional
- Stability: unverified → 0.87 ▲ functional
- MCP protocol: unverified → pass ▲ functional
- 14 Oct 26 +15
- Malware scan: unverified → pass ▲ security
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 4 Nov 2026 · Analysed pypi/piaso-mcp@0.1.1
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | pypi |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | genecell/PIASO-for-agents |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/genecell/PIASO-for-agents/.github/workflows/publish-mcp.yml@refs/heads/master |
| Rekor log index | 2991267389 |
| Predicate type | PyPI publish attestation https://docs.pypi.org/attestations/publish/v1 |
| Subject digest | sha256:32cfe4c07d5c770759d42038bf07b98c75e0342bf15240c3e7b65dd2faea0682 |
Background: How many MCP packages publish verified provenance →
Install scripts 1 script
| Hook | Tier | Command |
|---|---|---|
| build_backend | allowlisted | hatchling.build |
Background: Why install scripts are a supply-chain risk →
Dependencies 29 packages
| Packages resolved | 29 |
|---|---|
| No linked repository | 1 |
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
check_versions ~57
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').
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
compare_implementations ~62
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.
| Name | Type | Req | Description |
|---|---|---|---|
| function | string | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
get_api ~87
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).
| Name | Type | Req | Description |
|---|---|---|---|
| function | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
get_dataset ~48
One PIASO-data registry entry (live): title, url, md5, size, cells, features, counts layer, reference, tutorials that use it.
| Name | Type | Req | Description |
|---|---|---|---|
| name | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
get_markers ~48
Alias of query_marker_db (mirrors piaso.tl.getMarkers).
| Name | Type | Req | Description |
|---|---|---|---|
| cell_type | – | – | – |
| gene | – | – | – |
| limit | integer | – | – |
| species | – | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
list_datasets ~58
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.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
list_studies ~32
List the studies available in PIASOmarkerDB (proxies the live API; 36 at last check).
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
list_tutorials ~120
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.
| Name | Type | Req | Description |
|---|---|---|---|
| component | – | – | – |
| topic | – | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
query_marker_db ~133
Query the live PIASOmarkerDB for cell-type marker genes (proxies the piaso.org REST API). Works with zero packages installed, and is the programmatic path for R / non-Python users. Returns rows with: cell_type, condition, gene, species, specificity_score (a COSG score), study_publication, tissue. Cell-type names must match the study's vocabulary exactly. Requires network access to piaso.org.
| Name | Type | Req | Description |
|---|---|---|---|
| cell_type | – | – | – |
| gene | – | – | – |
| limit | integer | – | – |
| species | – | – | – |
| study | – | – | – |
| tissue | – | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
resolve_install ~84
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.
| Name | Type | Req | Description |
|---|---|---|---|
| components | array | yes | – |
| language | string | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
search_docs ~102
Search the PIASO ecosystem knowledge pack (works with zero packages installed). Covers PIASO, COSG/COSGR, cytome (Python + R), LARIS, Emergene, cytorete, PIASO-data, the cross-component decision rules, gotchas and the piaso.org tutorial index. Returns the most relevant sections for `query`.
| Name | Type | Req | Description |
|---|---|---|---|
| max_results | integer | – | – |
| query | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
version_matrix ~41
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.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
How do I install the io.github.genecell/piaso-mcp server?
io.github.genecell/piaso-mcp runs locally as a PyPI package, launched with uvx piaso-mcp. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
pypi · piaso-mcp
claude mcp add genecell-piaso-mcp -- uvx piaso-mcp
What is the io.github.genecell/piaso-mcp server?
io.github.genecell/piaso-mcp is listed in the public MCP registry as io.github.genecell/piaso-mcp. PIASO single-cell ecosystem docs (PIASO, COSG, cytome, LARIS, cytorete) + live PIASOmarkerDB. This page covers its PyPI package (piaso-mcp).
Is the io.github.genecell/piaso-mcp server safe to use?
io.github.genecell/piaso-mcp scores 73 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 4 November 2026. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the io.github.genecell/piaso-mcp server expose?
io.github.genecell/piaso-mcp exposes 12 tools: search_docs, get_api, compare_implementations, resolve_install, list_tutorials, and 7 more. Their descriptions and schemas cost roughly 872 tokens of context every time the server is loaded.
Is the io.github.genecell/piaso-mcp server still maintained?
io.github.genecell/piaso-mcp is still listed as active in the MCP registry. We last reached this channel on 4 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the io.github.genecell/piaso-mcp server under?
io.github.genecell/piaso-mcp declares the BSD-3-Clause licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.