Skill: cewinharhar/lobster-bio-use (version 1.0.1)

--- 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 ```bash curl -fsSL https://install.lobsterbio.com | bash ``` ### Windows (PowerShell) ```powershell irm https://install.lobsterbio.com/windows | iex ``` ### Manual install (any platform) ```bash 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](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 ```bash lobster chat # Start interactive session lobster chat --workspace ./myproject # Custom workspace lobster chat --reasoning # Enable detailed reasoning ``` ### Single Query ```bash 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 ```bash # 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 ```bash # 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


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