Perform quality control on single-cell RNA-seq data (.h5ad, 10x .h5, or 10x directories) using scverse best practices, MAD-based filtering (log1p counts/genes, high-tail MT%), and generate filtered AnnData plus QC plots and summary JSON. Use when users request scRNA-seq QC, filtering low-quality cells, data quality assessment, or QC visualizations.
AI-powered virtual laboratory orchestrating multi-agent scientific research teams for autonomous hypothesis generation, experimental design, and validation in biomedical research.
AI-powered time-resolved cryo-EM analysis for capturing protein dynamics, drug-binding kinetics, and conformational transitions for dynamics-based drug discovery.
AI-powered integration of cryo-EM structural data with generative AI and molecular dynamics for structure-based drug design targeting flexible proteins and membrane complexes.
Assemble and purify macromolecular complexes for structural biology. Use when the user asks about gel filtration, complex assembly, SEC purification, elongation complexes, calculating stoichiometry, or interpreting A260/A280 ratios.
Race condition and TOCTOU detection — database races, file system races, double-spend, and atomicity failures
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
Playwright CLI browser automation for AI agents. Navigate pages, take screenshots, fill forms, click elements from the command line. Use when automating browser tasks with shell access. Prefer over Playwright MCP (4-10x more token-efficient).
Rich terminal rendering of directive-flavored markdown. Panels, trees, columns, callouts, mermaid diagrams, syntax-highlighted code, diffs, charts, KPI tiles, timelines, tasklists, and inline badges — rendered as ANSI output or displayed in a tmux side pane. Use when producing visual output, diagrams, or structured terminal displays.
Browser automation and UI validation via the capture CLI. Interact with pages using accessibility-driven click, type, screenshot, a11y tree, JS exec, and HAR recording over CDP. Use when validating UI state, testing features in the browser, or manipulating a running web app.
Guide to creating CLI tools and scripts that augment Claude Code. Use when building bin/ executables, automation scripts, hook handlers, or tooling that abstracts repeated agent workflows.
Guide to writing slash commands for Claude Code. Use when creating commands that set mode, constraints, or workflows invoked via /command-name.
Route `/codex ...` requests to the local Codex CLI for one-shot autonomous execution. Use when the user explicitly invokes `/codex` or asks to hand a task off to Codex. Preserves the prompt verbatim, handles non-git directories, captures failures cleanly, and returns Codex's final message.
Tech pack description, available commands, and getting-started guide for fullstack-typescript.
Validate ADR relationships, detect orphaned references, and check domain consistency
List all ADRs with title, status, date, and domain in a markdown table
