compbioagent-explorer

name: compbioagent-explorer description: scRNA-seq Explorer keywords: - single-cell - visualization - web-app - cellxgene - exploration measurable_outcome: Launch a local web instance for interactive scRNA-seq exploration and generate 3+ custom visualizations per session. license: MIT metadata: author: CompBioAgent Team version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - web_fetch

CompBioAgent (Single-Cell Explorer)

An LLM-powered web application for single-cell RNA-seq data exploration, integrating with CellDepot and Cellxgene VIP.

When to Use

• Interactive Exploration: When you need to visually explore a dataset without writing code.
• Hypothesis Generation: Quickly checking expression of specific markers across clusters.
• Sharing: Presenting data to non-computational collaborators.

Core Capabilities

1. Natural Language Querying: "Show me the expression of TP53 in the B-cell cluster."
2. Cellxgene Integration: Leverages robust visualization tools.
3. Data Integration: Connects with CellDepot for dataset retrieval.

Workflow

1. Setup: pip install compbioagent.
2. Launch: compbioagent start --data ./data.h5ad.
3. Interact: Open the local URL (e.g., http://localhost:8050) and chat with the agent to generate plots.

Example Usage

User: "Launch the explorer for my kidney dataset."

Agent Action:

compbioagent launch --port 8080 --data ./kidney_atlas.h5ad