# CASSIA

> CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

- **URL**: https://www.freshcrate.ai/projects/CASSIA
- **Author**: ElliotXie
- **Category**: Frameworks
- **Latest version**: `v1.3.1` (2026-03-23)
- **License**: MIT
- **Source**: https://github.com/ElliotXie/CASSIA
- **Homepage**: https://elliotxie.github.io/CASSIA/
- **Language**: Python
- **GitHub**: 89 stars, 6 forks
- **Registry**: github
- **Tags**: `ai4science`, `annotation`, `bioinformatics`, `cell-annotation`, `llm`, `multiagent-systems`, `prompt-engineering`, `python`, `retrieved-augmented-generation`

## Description

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

## Recent releases

| Version | Date | Urgency | Changes |
| --- | --- | --- | --- |
| `v1.3.1` | 2026-03-23 | Medium | ## CASSIA v1.3.1  ### 🚀 New Features - **Enhanced Gene ID Conversion** — Improved Ensembl/Entrez ID to gene symbol conversion with auto-detection of species and Ensembl REST API fallback - **Scanpy Support** — Native support for Scanpy AnnData objects and `rank_genes_groups` output format - **Additional Ranking Methods** — Support for more differential expression ranking methods beyond FindAllMarkers - **Custom Provider Support** — Configure custom OpenAI-compatible API endpoints and local LLMs |
| `v1.2.0` | 2025-10-03 | Low | - Improved function output for clearer results. - Better file organization for easier navigation. - Fixed several bugs and stability issues. - Added Smart API matching to streamline connections with different LLM APIs. |
| `v1.1.0` | 2025-04-18 | Low | 🐛 Bug Fixes **Subclustering Agent Bug Fix** Resolved an issue in the subclustering agent. The agent now performs as expected.  ✨ New Features **Automatic Annotation Scoring Agent** Introduced a new agent that automatically scores annotations by comparing them with a provided gold standard. This addition helps streamline evaluation workflows and ensures consistent scoring for annotation quality checks. |
| `CASSIA` | 2024-11-27 | Low | 1.0.0 |

## Dependency audit

- **Score**: 100/100
- **Total deps**: 0
- **Resolved**: 0
- **Unresolved**: 0
- **License conflicts**: 0
- **Warnings**: 0
- **Scanned**: 2026-04-27

## Citation

- HTML: https://www.freshcrate.ai/projects/CASSIA
- Markdown: https://www.freshcrate.ai/projects/CASSIA.md
- Dependencies JSON: https://www.freshcrate.ai/api/projects/CASSIA/deps

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