Lobster AI Usage Guide

---

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.

---

# 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

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](references/cli-commands.md) |

| **Single-cell analysis** | [references/single-cell-workflow.md](references/single-cell-workflow.md) |

| **Bulk RNA-seq analysis** | [references/bulk-rnaseq-workflow.md](references/bulk-rnaseq-workflow.md) |

| **Literature & datasets** | [references/research-workflow.md](references/research-workflow.md) |

| **Visualization** | [references/visualization.md](references/visualization.md) |

| **Available agents** | [references/agents.md](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: