LobsterBio - Use

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name: lobster-use description: | 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.

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Lobster 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:

| Agent | Handles | |-------|---------| | Supervisor | Routes queries, coordinates agents | | Research Agent | PubMed search, GEO discovery, paper extraction | | Data Expert | File loading, format conversion, downloads | | Transcriptomics Expert | scRNA-seq: QC, clustering, markers | | DE Analysis Expert | Differential expression, statistical testing | | Annotation Expert | Cell type annotation, gene set enrichment | | Visualization Expert | UMAP, heatmaps, volcano plots | | Proteomics Expert | Mass spec analysis [alpha] | | Genomics Expert | VCF, GWAS, variant analysis [alpha] | | ML Expert | Embeddings, classification [alpha] |

Workspace & Outputs

Default workspace: .lobster_workspace/

Output files: | Extension | Content | |-----------|---------| | .h5ad | Processed AnnData objects | | .html | Interactive visualizations | | .png | Publication-ready plots | | .csv | Exported tables | | .json | Metadata, provenance |

Managing outputs:

/files              # List all outputs
/plots              # View visualizations
/open results.html  # Open in browser
/read summary.csv   # Preview file contents

Typical Workflow

# 1. Start session
lobster chat --workspace ./my_analysis
2. Load or download data
"Download GSE109564 from GEO"
or
/workspace load my_data.h5ad
3. Quality control
"Run quality control and show me the metrics"
4. Analysis
"Filter low-quality cells, normalize, and cluster"
5. Interpretation
"Identify cell types and find marker genes"
6. Visualization
"Create UMAP colored by cell type"
/plots
7. Export
"Export marker genes to CSV"
/save

Troubleshooting Quick Reference

| Issue | Check | |-------|-------| | Lobster not responding | lobster config-test | | No data loaded | /data to verify, /workspace list to see available | | Analysis fails | Try with --reasoning flag | | Missing outputs | Check /files and workspace directory |

Documentation

Online docs: docs.omics-os.com

Key sections:

Guides → CLI Commands

Guides → Data Analysis Workflows

Tutorials → Single-Cell RNA-seq

Agents → Package documentation