cff-version: 1.2.0
message: "If you use this software, please cite it as below."
type: software
title: "ChatSpatial: Agentic Workflow Orchestration for Spatial Transcriptomics Analysis"
version: "0.2.1"
date-released: "2025-08-26"
url: "https://github.com/cafferychen777/ChatSpatial"
repository-code: "https://github.com/cafferychen777/ChatSpatial"
license: MIT
authors:
- family-names: "Yang"
given-names: "Caffery(Chen)"
orcid: "https://orcid.org/0009-0009-9151-2901"
affiliation: "Texas A&M University"
email: "cafferychen777@tamu.edu"
abstract: >-
ChatSpatial is an agentic workflow orchestration platform that eliminates the
"implementation tax" in spatial transcriptomics analysis. Built on the Model
Context Protocol (MCP), it integrates 60 state-of-the-art methods from fragmented
Python and R ecosystems into a unified conversational interface, enabling researchers
to execute complex multi-tool workflows through natural language without writing code.
Unlike autonomous agents, ChatSpatial prioritizes human-steered discovery through
schema-enforced tool-calling that ensures reproducibility and analytical fidelity.
The platform eliminates cross-platform data conversion barriers, allowing researchers
to focus on biological insight rather than software engineering.
keywords:
- spatial transcriptomics
- artificial intelligence
- bioinformatics integration
- natural language processing
- computational biology
- software platform
- cancer research
- model context protocol
- agentic workflow
preferred-citation:
type: software
title: "ChatSpatial: Agentic Workflow Orchestration for Spatial Transcriptomics Analysis"
authors:
- family-names: "Yang"
given-names: "Caffery(Chen)"
orcid: "https://orcid.org/0009-0009-9151-2901"
affiliation: "Texas A&M University"
email: "cafferychen777@tamu.edu"
version: "0.2.1"
date-released: "2025-08-26"
url: "https://github.com/cafferychen777/ChatSpatial"
repository-code: "https://github.com/cafferychen777/ChatSpatial"
license: MIT
