Lobster AI combines specialized AI agents with open-source bioinformatics tools to analyze multi-omics data through natural language. Describe your analysis needs - no coding required.
Perfect for:
🧬 Bioinformatics researchers analyzing RNA-seq data
❯ Find papers about CRISPR screens in cancer and extract their GEO datasets
Found 47 papers with 23 associated GEO datasets
Extracted methods from 12 papers with full-text access
Cached metadata for all datasets in workspace
📈 Visualization
Publication-ready figures with natural language
❯ Create a UMAP colored by cell type with cluster labels
Generated interactive UMAP visualization
Saved as: geo_gse109564_umap_celltype.html
Also exported as PNG for publications
Lobster integrates with Claude Code as an Agent Skill, allowing you to run bioinformatics analyses directly from your development environment.
Quick Setup
# 1. Install Lobster
uv pip install lobster-ai
lobster init
# 2. Install Lobster Skill for Claude Code
curl -fsSL https://raw.githubusercontent.com/the-omics-os/lobster-local/main/claude-skill/SKILL.md \
-o ~/.claude/skills/lobster/SKILL.md --create-dirs
# 3. Start Claude Code
claude
Usage Examples
Claude Code will automatically invoke Lobster when you mention bioinformatics tasks:
# In Claude Code, just ask naturally:
You: "Analyze the single-cell dataset in data/counts.h5ad"
Claude: I'll use Lobster to analyze this single-cell dataset...
[Invokes: lobster query "analyze data/counts.h5ad..."]
You: "Download GSE109564 and run quality control"
Claude: I'll use Lobster to download and analyze this dataset...
[Invokes: lobster query "download GSE109564 and run QC"]
You: "Find papers about CRISPR screens in cancer"
Claude: I'll use Lobster to search the literature...
[Invokes: lobster query "search pubmed for CRISPR screens cancer"]
What this enables:
🧬 Run bioinformatics analyses without leaving your IDE
📊 Extract data and generate reports programmatically
🔄 Combine Lobster with your development workflow
🤖 Let Claude handle the complexity of bioinformatics commands
