ChatSpatial

Name: ChatSpatial Review
Item: ChatSpatial
Rating: 3.1
Author: Aaron Matthews

Skill Development Usable

Works inClaude Code

Usable Scanned — metadata only

Enables bioinformatics teams to perform complex spatial transcriptomics analysis without deep programming expertise, reducing analysis iteration time and low…

ChatSpatial is an MCP server for running spatial transcriptomics analysis through plain-language requests. Instead of generating ad-hoc analysis scripts, it has the model pick tools and parameters from a curated registry: 20 schema-validated MCP tools that orchestrate 65 analysis methods across 15 categories, including preprocessing, spatial-domain identification, deconvolution, cell-cell communication, and trajectory inference. It works with any MCP-compatible client (Claude Code, Claude Desktop, and others) and supports 10x Visium, Xenium, Slide-seq v2, MERFISH, and seqFISH data.

Ask Claude to identify spatial gene expression patterns in tissue samples using natural language queries.
Generate visualizations of transcriptomic data across tissue coordinates without writing analysis code.
Automate clustering and annotation of spatial transcriptomics datasets through conversational instructions.

43 starsMIT (commercial OK)FreeQuick setup

Usable rating — This tool is functional but has notable gaps. Review the evaluation notes below before deploying.

Why it matters

Enables bioinformatics teams to perform complex spatial transcriptomics analysis without deep programming expertise, reducing analysis iteration time and lowering the barrier for non-computational researchers.

Best for

Bioinformatics researchers and genomics labs conducting spatial transcriptomics studies needing accessible analysis interfaces.

Works in

Claude Code Claude Cowork Claude Chat

Source

https://github.com/cafferychen777/ChatSpatial

By cafferychen777

How to Get It

Option 1: Claude Desktop App (Code Mode)Click the + button next to the prompt box → Plugins → Add plugin. Search and click Install. Skills work in Claude Code only.

Option 2: Paste into Claude CodeCopy the command below and paste it into your conversation. Claude will install it.

Command

pip install chatspatial

Tip: Paste this into a Claude Code conversation. Verify command matches your Claude Code version.

First thing to try

After installing, paste this into Claude:

Identify spatial gene expression patterns in tissue samples using natural language queries

CostFree

Trust Signals Auto-scanned

Stars43Contributors3Last updated2026-08-14LicenseMIT (OK for commercial use)Known CVEsNone foundSources: GitHub Advisory Database + OSV.dev · Scanned 2026-08-14 · scanner v1

Reviewer notes

Auto-scanned review. These are observations, not a security certification.

catalog_hygiene stale-eval refresh: Scored from trust signals (evidence-eval-v1): 43 GitHub stars; 3 contributors; last commit 4d ago; license MIT.

Things to check

Scanned, not hands-on tested — this entry was auto-scanned from public metadata (GitHub metrics, license, security flags). No reviewer has run it, and no tool-specific limitations have been documented yet.

How to evaluate tools before deploying →

Data shown here comes from public APIs and automated scanning. Reviewer notes reflect one person's experience. This is not a security certification or legal recommendation. Always evaluate tools according to your own organization's policies.

Evaluation Scores

Evaluation

Ease of Use

3/5

Versatility

2/5

Reliability

4/5

Security

4/5

Overall score3.15 / 5.00 UsableEvaluatedAug 2026

catalog_hygiene stale-eval refresh: Scored from trust signals (evidence-eval-v1): 43 GitHub stars; 3 contributors; last commit 4d ago; license MIT.

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