Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

Query FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources. Access GDP, unemployment, inflation, interest rates, exchange rates, housing, and regional data. Use for macroeconomic analysis, financial research, policy studies, economic forecasting, and academic research requiring U.S. and international economic indicators.

Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

Create production-ready FastAPI projects with async patterns, dependency injection, and comprehensive error handling. Use when building new FastAPI applications or setting up backend API projects.

Create, alter, and validate Snowflake semantic views using Snowflake CLI (snow). Use when asked to build or troubleshoot semantic views/semantic layer definitions with CREATE/ALTER SEMANTIC VIEW, to validate semantic-view DDL against Snowflake via CLI, or to guide Snowflake CLI installation and connection setup.

Use only when the user explicitly asks to stage, commit, push, and open a GitHub pull request in one flow using the GitHub CLI (`gh`).

Comprehensive PDF manipulation toolkit for extracting text and tables, creating new PDFs, merging/splitting documents, and handling forms. When Claude needs to fill in a PDF form or programmatically process, generate, or analyze PDF documents at scale.