Windows (PowerShell):

irm https://install.lobsterbio.com/windows | iex

uv (recommended manual install):

uv tool install 'lobster-ai[full,anthropic]'
lobster init

pip:

pip install 'lobster-ai[full]'
lobster init

Upgrade:

uv tool upgrade lobster-ai    # uv
pip install -U lobster-ai      # pip

Create custom agents for any domain. Agents plug in via Python entry points — discovered automatically, no core changes needed.

Install the lobster-dev skill to teach your coding agent the full architecture:

curl -fsSL https://skills.lobsterbio.com | bash

Then ask your coding agent: "Create a Lobster agent for [your domain]" — it knows the package structure, AGENT_CONFIG pattern, factory function, tool design, testing, and the 28-step checklist.

Transcriptomics

• Single-cell RNA-seq: QC, doublet detection (Scrublet), batch integration (Harmony/scVI), clustering, cell type annotation, trajectory inference (DPT/PAGA)
• Bulk RNA-seq: Salmon/kallisto/featureCounts import, sample QC, batch detection, normalization (DESeq2/VST/CPM), DE with PyDESeq2, GSEA, publication-ready export

Genomics

• GWAS: VCF/PLINK import, LD pruning, kinship, association testing, result clumping
• Clinical: variant annotation (VEP), gnomAD frequencies, ClinVar pathogenicity, variant prioritization

Proteomics

• Mass spec: MaxQuant/DIA-NN/Spectronaut import, PTM analysis, peptide-to-protein rollup, batch correction
• Affinity: Olink NPX/SomaScan ADAT/Luminex MFI import, LOD quality, bridge normalization
• Downstream: GO/Reactome/KEGG enrichment, kinase enrichment (KSEA), STRING PPI, biomarker panel selection

Metabolomics

• LC-MS, GC-MS, NMR with auto-detection
• QC (RSD, TIC), filtering, imputation, normalization (PQN/TIC/IS)
• PCA, PLS-DA, OPLS-DA, m/z annotation (HMDB/KEGG), lipid class analysis

Machine Learning

• Feature selection (stability selection, LASSO, variance filter)
• Survival analysis (Cox models, Kaplan-Meier, risk stratification)
• Cross-validation, SHAP interpretability, multi-omics integration (MOFA)

Research & Metadata

• Literature discovery (PubMed, PMC, GEO, PRIDE, MetaboLights)
• Dataset download orchestration, metadata harmonization, sample filtering

Lobster supports 5 LLM providers. Configure via lobster init or environment variables.

Teach your coding agents (Claude Code, Codex, Gemini CLI, OpenClaw) to use Lobster:

curl -fsSL https://skills.lobsterbio.com | bash

Installs two skills:

• lobster-use — End-user workflows (search PubMed, analyze cells, RNA-seq)
• lobster-dev — Developer guide (create agents, extend services, testing)

Set during lobster init or manually: