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    "name": "LobsterBio - Use",
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      "references/bulk-rnaseq-workflow.md",
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      "references/agents.md",
      "references/visualization.md",
      "references/single-cell-workflow.md"
    ],
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      "Download the package from Yavira.",
      "Extract the archive and review SKILL.md first.",
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      "summary": "Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.",
      "steps": [
        "Download the package from Yavira.",
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        "Paste one of the prompts below and point your agent at the extracted folder."
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          "label": "New install",
          "body": "I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Tell me what you changed and call out any manual steps you could not complete."
        },
        {
          "label": "Upgrade existing",
          "body": "I downloaded an updated skill package from Yavira. Read SKILL.md from the extracted folder, compare it with my current installation, and upgrade it while preserving any custom configuration unless the package docs explicitly say otherwise. Summarize what changed and any follow-up checks I should run."
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        "Use the Yavira download entry.",
        "Review SKILL.md after the package is downloaded.",
        "Confirm the extracted package contains the expected setup assets."
      ],
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        "Confirm the extracted package includes the expected docs or setup files.",
        "Validate the skill or prompts are available in your target agent workspace.",
        "Capture any manual follow-up steps the agent could not complete."
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    "agentPageUrl": "https://openagent3.xyz/skills/lobster-bio-use/agent",
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  "agentAssist": {
    "summary": "Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.",
    "steps": [
      "Download the package from Yavira.",
      "Extract it into a folder your agent can access.",
      "Paste one of the prompts below and point your agent at the extracted folder."
    ],
    "prompts": [
      {
        "label": "New install",
        "body": "I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Tell me what you changed and call out any manual steps you could not complete."
      },
      {
        "label": "Upgrade existing",
        "body": "I downloaded an updated skill package from Yavira. Read SKILL.md from the extracted folder, compare it with my current installation, and upgrade it while preserving any custom configuration unless the package docs explicitly say otherwise. Summarize what changed and any follow-up checks I should run."
      }
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  "documentation": {
    "source": "clawhub",
    "primaryDoc": "SKILL.md",
    "sections": [
      {
        "title": "Lobster AI Usage Guide",
        "body": "Lobster AI is a multi-agent bioinformatics platform. You interact via natural language\nor slash commands — Lobster routes to specialist agents automatically."
      },
      {
        "title": "Installation",
        "body": "If Lobster is not installed, guide the user to the right command for their platform:"
      },
      {
        "title": "macOS / Linux",
        "body": "curl -fsSL https://install.lobsterbio.com | bash"
      },
      {
        "title": "Windows (PowerShell)",
        "body": "irm https://install.lobsterbio.com/windows | iex"
      },
      {
        "title": "Manual install (any platform)",
        "body": "uv tool install 'lobster-ai[full,anthropic]' && lobster init\n# or: pip install 'lobster-ai[full]' && lobster init\n\nAfter install, lobster init configures API keys and selects agent packages."
      },
      {
        "title": "Upgrading",
        "body": "uv tool: uv tool upgrade lobster-ai\npip: pip install --upgrade lobster-ai"
      },
      {
        "title": "Adding Agents (uv tool installs)",
        "body": "Users with uv tool installs add agents via:\nuv tool install lobster-ai --with lobster-transcriptomics --with lobster-proteomics\nRunning lobster init will guide this process and generate the command."
      },
      {
        "title": "Quick Reference",
        "body": "TaskReferenceCLI commandsreferences/cli-commands.mdSingle-cell analysisreferences/single-cell-workflow.mdBulk RNA-seq analysisreferences/bulk-rnaseq-workflow.mdLiterature & datasetsreferences/research-workflow.mdVisualizationreferences/visualization.mdAvailable agentsreferences/agents.md"
      },
      {
        "title": "Interactive Chat",
        "body": "lobster chat                          # Start interactive session\nlobster chat --workspace ./myproject  # Custom workspace\nlobster chat --reasoning              # Enable detailed reasoning"
      },
      {
        "title": "Single Query",
        "body": "lobster query \"Your request\"\nlobster query --session-id latest \"Follow-up request\""
      },
      {
        "title": "Natural Language (Primary)",
        "body": "Just describe what you want:\n\n\"Download GSE109564 and run quality control\"\n\"Cluster the cells and find marker genes\"\n\"Compare hepatocytes vs stellate cells\""
      },
      {
        "title": "Slash Commands (System Operations)",
        "body": "/data                    # Show loaded data info\n/files                   # List workspace files\n/workspace list          # List available datasets\n/workspace load 1        # Load dataset by index\n/plots                   # Show generated visualizations\n/save                    # Save current session\n/status                  # Show system status\n/help                    # All commands"
      },
      {
        "title": "Session Continuity",
        "body": "# Start named session\nlobster query --session-id \"my_analysis\" \"Load GSE109564\"\n\n# Continue with context\nlobster query --session-id latest \"Now cluster the cells\"\nlobster query --session-id latest \"Find markers for cluster 3\""
      },
      {
        "title": "Agent System",
        "body": "Lobster routes to specialist agents automatically:\n\nAgentHandlesSupervisorRoutes queries, coordinates agentsResearch AgentPubMed search, GEO discovery, paper extractionData ExpertFile loading, format conversion, downloadsTranscriptomics ExpertscRNA-seq: QC, clustering, markersDE Analysis ExpertDifferential expression, statistical testingAnnotation ExpertCell type annotation, gene set enrichmentVisualization ExpertUMAP, heatmaps, volcano plotsProteomics ExpertMass spec analysis [alpha]Genomics ExpertVCF, GWAS, variant analysis [alpha]ML ExpertEmbeddings, classification [alpha]"
      },
      {
        "title": "Workspace & Outputs",
        "body": "Default workspace: .lobster_workspace/\n\nOutput files:\n\nExtensionContent.h5adProcessed AnnData objects.htmlInteractive visualizations.pngPublication-ready plots.csvExported tables.jsonMetadata, provenance\n\nManaging outputs:\n\n/files              # List all outputs\n/plots              # View visualizations\n/open results.html  # Open in browser\n/read summary.csv   # Preview file contents"
      },
      {
        "title": "Typical Workflow",
        "body": "# 1. Start session\nlobster chat --workspace ./my_analysis\n\n# 2. Load or download data\n\"Download GSE109564 from GEO\"\n# or\n/workspace load my_data.h5ad\n\n# 3. Quality control\n\"Run quality control and show me the metrics\"\n\n# 4. Analysis\n\"Filter low-quality cells, normalize, and cluster\"\n\n# 5. Interpretation\n\"Identify cell types and find marker genes\"\n\n# 6. Visualization\n\"Create UMAP colored by cell type\"\n/plots\n\n# 7. Export\n\"Export marker genes to CSV\"\n/save"
      },
      {
        "title": "Troubleshooting Quick Reference",
        "body": "IssueCheckLobster not respondinglobster config-testNo data loaded/data to verify, /workspace list to see availableAnalysis failsTry with --reasoning flagMissing outputsCheck /files and workspace directory"
      },
      {
        "title": "Documentation",
        "body": "Online docs: docs.omics-os.com\n\nKey sections:\n\nGuides → CLI Commands\nGuides → Data Analysis Workflows\nTutorials → Single-Cell RNA-seq\nAgents → Package documentation"
      }
    ],
    "body": "Lobster AI Usage Guide\n\nLobster AI is a multi-agent bioinformatics platform. You interact via natural language or slash commands — Lobster routes to specialist agents automatically.\n\nInstallation\n\nIf Lobster is not installed, guide the user to the right command for their platform:\n\nmacOS / Linux\ncurl -fsSL https://install.lobsterbio.com | bash\n\nWindows (PowerShell)\nirm https://install.lobsterbio.com/windows | iex\n\nManual install (any platform)\nuv tool install 'lobster-ai[full,anthropic]' && lobster init\n# or: pip install 'lobster-ai[full]' && lobster init\n\n\nAfter install, lobster init configures API keys and selects agent packages.\n\nUpgrading\nuv tool: uv tool upgrade lobster-ai\npip: pip install --upgrade lobster-ai\nAdding Agents (uv tool installs)\n\nUsers 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.\n\nQuick Reference\nTask\tReference\nCLI commands\treferences/cli-commands.md\nSingle-cell analysis\treferences/single-cell-workflow.md\nBulk RNA-seq analysis\treferences/bulk-rnaseq-workflow.md\nLiterature & datasets\treferences/research-workflow.md\nVisualization\treferences/visualization.md\nAvailable agents\treferences/agents.md\nInteraction Modes\nInteractive Chat\nlobster chat                          # Start interactive session\nlobster chat --workspace ./myproject  # Custom workspace\nlobster chat --reasoning              # Enable detailed reasoning\n\nSingle Query\nlobster query \"Your request\"\nlobster query --session-id latest \"Follow-up request\"\n\nCore Patterns\nNatural Language (Primary)\n\nJust describe what you want:\n\n\"Download GSE109564 and run quality control\"\n\"Cluster the cells and find marker genes\"\n\"Compare hepatocytes vs stellate cells\"\n\nSlash Commands (System Operations)\n/data                    # Show loaded data info\n/files                   # List workspace files\n/workspace list          # List available datasets\n/workspace load 1        # Load dataset by index\n/plots                   # Show generated visualizations\n/save                    # Save current session\n/status                  # Show system status\n/help                    # All commands\n\nSession Continuity\n# Start named session\nlobster query --session-id \"my_analysis\" \"Load GSE109564\"\n\n# Continue with context\nlobster query --session-id latest \"Now cluster the cells\"\nlobster query --session-id latest \"Find markers for cluster 3\"\n\nAgent System\n\nLobster routes to specialist agents automatically:\n\nAgent\tHandles\nSupervisor\tRoutes queries, coordinates agents\nResearch Agent\tPubMed search, GEO discovery, paper extraction\nData Expert\tFile loading, format conversion, downloads\nTranscriptomics Expert\tscRNA-seq: QC, clustering, markers\nDE Analysis Expert\tDifferential expression, statistical testing\nAnnotation Expert\tCell type annotation, gene set enrichment\nVisualization Expert\tUMAP, heatmaps, volcano plots\nProteomics Expert\tMass spec analysis [alpha]\nGenomics Expert\tVCF, GWAS, variant analysis [alpha]\nML Expert\tEmbeddings, classification [alpha]\nWorkspace & Outputs\n\nDefault workspace: .lobster_workspace/\n\nOutput files:\n\nExtension\tContent\n.h5ad\tProcessed AnnData objects\n.html\tInteractive visualizations\n.png\tPublication-ready plots\n.csv\tExported tables\n.json\tMetadata, provenance\n\nManaging outputs:\n\n/files              # List all outputs\n/plots              # View visualizations\n/open results.html  # Open in browser\n/read summary.csv   # Preview file contents\n\nTypical Workflow\n# 1. Start session\nlobster chat --workspace ./my_analysis\n\n# 2. Load or download data\n\"Download GSE109564 from GEO\"\n# or\n/workspace load my_data.h5ad\n\n# 3. Quality control\n\"Run quality control and show me the metrics\"\n\n# 4. Analysis\n\"Filter low-quality cells, normalize, and cluster\"\n\n# 5. Interpretation\n\"Identify cell types and find marker genes\"\n\n# 6. Visualization\n\"Create UMAP colored by cell type\"\n/plots\n\n# 7. Export\n\"Export marker genes to CSV\"\n/save\n\nTroubleshooting Quick Reference\nIssue\tCheck\nLobster not responding\tlobster config-test\nNo data loaded\t/data to verify, /workspace list to see available\nAnalysis fails\tTry with --reasoning flag\nMissing outputs\tCheck /files and workspace directory\nDocumentation\n\nOnline docs: docs.omics-os.com\n\nKey sections:\n\nGuides → CLI Commands\nGuides → Data Analysis Workflows\nTutorials → Single-Cell RNA-seq\nAgents → Package documentation"
  },
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    "sourceLabel": "tencent",
    "provenanceUrl": "https://clawhub.ai/cewinharhar/lobster-bio-use",
    "publisherUrl": "https://clawhub.ai/cewinharhar/lobster-bio-use",
    "owner": "cewinharhar",
    "version": "1.0.1",
    "license": null,
    "verificationStatus": "Indexed source record"
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