lobster-bioinformatics

When to use this Skill

Use Lobster when the user asks to:

• Analyze single-cell RNA-seq data (QC, clustering, annotation, markers)
• Perform bulk RNA-seq analysis (differential expression, complex designs)
• Search scientific literature (PubMed, PMC, full-text retrieval)
• Discover datasets (GEO, SRA, ENA (free) and PRIDE, MASSive (cloud))
• Run quality control on biological data
• Generate bioinformatics visualizations (UMAP, volcano plots, heatmaps)
• Download and process biological datasets
• Work with H5AD, CSV, Excel, 10X formats
• Extract methods or metadata from papers

Requirements

Lobster must be installed and configured:

## Pre-flight check (IMPORTANT)

**Before running any analysis, always verify Lobster is ready:**

Returns structured JSON:

This command validates:
- **LLM provider** - Ollama server running + models installed, or Anthropic/Bedrock API keys valid
- **NCBI API** - PubMed/GEO access (optional but recommended)
- **Workspace** - Directory writable for output files

**Expected output for a working setup:**

**If config-test fails:**

| Error | Solution |
|-------|----------|
| No LLM provider configured | Run `lobster init` |
| Ollama server not accessible | Start Ollama: `ollama serve` |
| Ollama: No models installed | After asking user - Install a model: `ollama pull gpt-oss:20b` |
| Anthropic/Bedrock API error | Check API key validity in `.env` |
| NCBI API not configured | Add `NCBI_API_KEY` to `.env` (optional) |
| Workspace not writable | Check directory permissions |

**Quick status checks:**
```bash