lobster-use
Analyze biological data using Lobster AI — single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. USE THIS SKILL WHEN: - Analyzing single-cell or bulk RNA-seq data - Searching PubMed/GEO for papers or datasets - Running quality control on biological data - Clustering cells, finding markers, differential expression - Creating publication-quality visualizations - Working with H5AD, CSV, 10X, GEO/SRA accessions TRIGGER PHRASES: "analyze cells", "search PubMed", "download GEO", "run QC", "cluster", "find markers", "differential expression", "UMAP", "volcano plot", "single-cell", "RNA-seq", "bioinformatics" ASSUMES: Lobster is installed and configured. For setup issues, tell user to run `lobster config-test` and fix any errors before proceeding.
Install via CLI (Recommended)
clawhub install openclaw/skills/skills/cewinharhar/lobster-bio-useLobster AI Usage Guide
Lobster AI is a multi-agent bioinformatics platform. You interact via natural language or slash commands — Lobster routes to specialist agents automatically.
Installation
If Lobster is not installed, guide the user to the right command for their platform:
macOS / Linux
curl -fsSL https://install.lobsterbio.com | bash
Windows (PowerShell)
irm https://install.lobsterbio.com/windows | iex
Manual install (any platform)
uv tool install 'lobster-ai[full,anthropic]' && lobster init
# or: pip install 'lobster-ai[full]' && lobster init
After install, lobster init configures API keys and selects agent packages.
Upgrading
- uv tool:
uv tool upgrade lobster-ai - pip:
pip install --upgrade lobster-ai
Adding Agents (uv tool installs)
Users with uv tool installs add agents via:
uv tool install lobster-ai --with lobster-transcriptomics --with lobster-proteomics
Running lobster init will guide this process and generate the command.
Quick Reference
| Task | Reference |
|---|---|
| CLI commands | references/cli-commands.md |
| Single-cell analysis | references/single-cell-workflow.md |
| Bulk RNA-seq analysis | references/bulk-rnaseq-workflow.md |
| Literature & datasets | references/research-workflow.md |
| Visualization | references/visualization.md |
| Available agents | references/agents.md |
Interaction Modes
Interactive Chat
lobster chat # Start interactive session
lobster chat --workspace ./myproject # Custom workspace
lobster chat --reasoning # Enable detailed reasoning
Single Query
lobster query "Your request"
lobster query --session-id latest "Follow-up request"
Core Patterns
Natural Language (Primary)
Just describe what you want:
"Download GSE109564 and run quality control"
"Cluster the cells and find marker genes"
"Compare hepatocytes vs stellate cells"
Slash Commands (System Operations)
/data # Show loaded data info
/files # List workspace files
/workspace list # List available datasets
/workspace load 1 # Load dataset by index
/plots # Show generated visualizations
/save # Save current session
/status # Show system status
/help # All commands
Session Continuity
# Start named session
lobster query --session-id "my_analysis" "Load GSE109564"
# Continue with context
lobster query --session-id latest "Now cluster the cells"
lobster query --session-id latest "Find markers for cluster 3"
Agent System
Lobster routes to specialist agents automatically:
Metadata
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Find the right skillPaste this into your clawhub.json to enable this plugin.
{
"plugins": {
"official-cewinharhar-lobster-bio-use": {
"enabled": true,
"auto_update": true
}
}
}Related Skills
lobster-use
Runs bioinformatics analysis with Lobster AI -- single-cell RNA-seq, bulk RNA-seq, genomics (VCF/GWAS), proteomics (mass spec/affinity), metabolomics (LC-MS/GC-MS/NMR), machine learning (feature selection, survival analysis), drug discovery, literature search, dataset discovery, and visualization. Use when working with biological data, omics analysis, or bioinformatics tasks. Covers: H5AD, CSV, VCF, PLINK, 10X, mzML formats, GEO/SRA/PRIDE/MetaboLights accessions. TRIGGER PHRASES: "analyze cells", "search PubMed", "download GEO", "run QC", "cluster", "find markers", "differential expression", "UMAP", "volcano plot", "single-cell", "RNA-seq", "VCF", "GWAS", "proteomics", "mass spec", "metabolomics", "MetaboLights", "LC-MS", "metabolite", "feature selection", "survival analysis", "biomarker", "bioinformatics", "drug discovery", "pharmacogenomics", "variant annotation" ASSUMES: Lobster is installed and configured. For setup issues, tell user to run `lobster config-test` and fix any errors before proceeding.
lobster-dev
Develop, extend, and contribute to Lobster AI — the multi-agent bioinformatics engine. Use when working on Lobster codebase, creating agents/services, understanding architecture, fixing bugs, adding features, or contributing to the open-source project. Trigger phrases: "add agent", "create service", "extend lobster", "contribute", "understand architecture", "how does X work in lobster", "fix bug", "add feature", "write tests", "lobster development", "agent development", "bioinformatics code"
lobster-dev
Develop, extend, and contribute to Lobster AI — the multi-agent self-extending bioinformatics engine. Use when working on Lobster codebase, creating agents/services, understanding architecture, fixing bugs, adding features, or contributing to the open-source project. IMPORTANT: Before creating new agents or packages, follow the planning workflow first (see "What To Do Based On Your Task" → planning-workflow.md). Trigger phrases: "add agent", "create service", "extend lobster", "contribute", "understand architecture", "how does X work in lobster", "fix bug", "add feature", "write tests", "lobster development", "agent development", "bioinformatics code", "build a new agent for", "add support for", "create plugin", "new domain"