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Agent Packages

Domain-specific agent packages for Lobster AI

Agent Packages

Lobster AI uses a modular architecture where domain expertise is provided by separate packages. Install only what you need.

Quick Install

# Core + all agents
pip install lobster-ai[full]

Available Packages

Stable

lobster-transcriptomics
FreeBeginner

Single-cell and bulk RNA-seq: QC, clustering, differential expression

Input
10X GenomicsH5ADCSVGEO
Output
QC ReportClustersUMAPDE Genes
Agents (3)
└── transcriptomics_expert — Workflow orchestration and delegation
├── annotation_expert — Cell type annotation and QC
└── de_analysis_expert — Differential expression analysis
pip install lobster-transcriptomics
lobster-research
FreeBeginner

Research planning: GEO dataset discovery and data loading

Input
GEO IDsKeywordsH5ADCSV
Output
Dataset MetadataLoaded DataAnalysis Plans
Agents (2)
├── research_agent — Literature discovery, PubMed/GEO search (online)
└── data_expert_agent — Download execution and data loading (offline)
pip install lobster-research
lobster-visualization
FreeBeginner

Publication-quality visualizations: UMAP, violin plots, heatmaps

Input
AnnDataDE ResultsCluster Labels
Output
UMAP PlotsViolin PlotsHeatmapsVolcano Plots
pip install lobster-visualization
lobster-metadata
FreeIntermediate

Publication queue processing: ID mapping, metadata filtering, batch operations

Input
PubMed IDsGEO IDsSRA IDsPublication Queue
Output
Unified CSVMapped IdentifiersFiltered Metadata
pip install lobster-metadata

Alpha

lobster-proteomics
FreeIntermediate

Mass spectrometry analysis: protein quantification and PTM detection

Input
MaxQuantDIA-NNSpectronautCSV
Output
Protein AbundancesDE ProteinsPTM Sites
pip install lobster-proteomics
lobster-genomics
FreeIntermediate

Variant analysis: VCF parsing, annotation, and GWAS

Input
VCFBCFgVCFPhenotype TSV
Output
Annotated VariantsManhattan PlotsGWAS Results
pip install lobster-genomics
lobster-ml
FreeAdvanced

Machine learning: embeddings, classification, and clustering

Input
AnnDataExpression MatricesFeature Tables
Output
EmbeddingsPredictionsModel Metrics
Agents (3)
└── machine_learning_expert — ML preparation and sub-agent routing
├── feature_selection_expert — Biomarker discovery and feature ranking
└── survival_analysis_expert — Cox models and Kaplan-Meier analysis
pip install lobster-ml
lobster-structural-viz
FreeAdvanced

Protein structure visualization: PyMOL, ChimeraX, interaction networks

Input
PDB FilesAlphaFold IDsUniProt IDs
Output
Structure RenderingsInteraction MapsAnalysis Reports
pip install lobster-structural-viz

Package Structure

Each agent package follows a standard structure:

lobster-\{domain\}/
  pyproject.toml
  lobster/
    agents/
      \{domain\}/
        __init__.py
        \{domain\}_expert.py
        config.py
        prompts.py

Tier System

All official Lobster agents are free and open source. The tier system exists for custom enterprise packages.

  • Free: All 8 official agent packages (13 agents)
  • Enterprise: Custom lobster-custom-* packages

All agents are included in pip install lobster-ai[full]. The tier infrastructure remains available for custom enterprise packages that need access control.

PreviousGenomics
NextMetadata

Component Registry

Plugin discovery via entry points with ComponentRegistry

Transcriptomics

Single-cell and bulk RNA-seq analysis agents

On this page

Agent PackagesQuick InstallAvailable PackagesStableAlphaPackage StructureTier System