monarch-database
Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup.
scvi-tools
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.
drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
shap
Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
simpy
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.
biopython
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
aeon
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
openalex-database
Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly works. Use for literature searches, research output analysis, citation analysis, and academic database queries.
primekg
Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
ena-database
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
pptx
Use this skill any time a .pptx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx file (even if the extracted content will be used elsewhere, like in an email or summary); editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates, layouts, speaker notes, or comments. Trigger whenever the user mentions \"deck,\" \"slides,\" \"presentation,\" or references a .pptx filename, regardless of what they plan to do with the content afterward. If a .pptx file needs to be opened, created, or touched, use this skill.
networkx
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
exploratory-data-analysis
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
scvelo
RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.
sympy
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
adaptyv
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
Analyzing AgentScope Library
This skill provides a way to retrieve information from the AgentScope library for analysis and decision-making.
A2UI_response_generator
A skill that can retrieve A2UI UI JSON schematics and UI templates that best show the response. This skill is essential and must be used before generating A2UI (Agent to UI) JSON responses.
security-threat-model
Repository-grounded threat modeling that enumerates trust boundaries, assets, attacker capabilities, abuse paths, and mitigations, and writes a concise Markdown threat model. Trigger only when the user explicitly asks to threat model a codebase or path, enumerate threats/abuse paths, or perform AppSec threat modeling. Do not trigger for general architecture summaries, code review, or non-security design work.
security-ownership-map
Analyze git repositories to build a security ownership topology (people-to-file), compute bus factor and sensitive-code ownership, and export CSV/JSON for graph databases and visualization. Trigger only when the user explicitly wants a security-oriented ownership or bus-factor analysis grounded in git history (for example: orphaned sensitive code, security maintainers, CODEOWNERS reality checks for risk, sensitive hotspots, or ownership clusters). Do not trigger for general maintainer lists or non-security ownership questions.
security-best-practices
Perform language and framework specific security best-practice reviews and suggest improvements. Trigger only when the user explicitly requests security best practices guidance, a security review/report, or secure-by-default coding help. Trigger only for supported languages (python, javascript/typescript, go). Do not trigger for general code review, debugging, or non-security tasks.
screenshot
Use when the user explicitly asks for a desktop or system screenshot (full screen, specific app or window, or a pixel region), or when tool-specific capture capabilities are unavailable and an OS-level capture is needed.
figma-code-connect-components
Connects Figma design components to code components using Code Connect mapping tools. Use when user says "code connect", "connect this component to code", "map this component", "link component to code", "create code connect mapping", or wants to establish mappings between Figma designs and code implementations. For canvas writes via `use_figma`, use `figma-use`.
figma-create-design-system-rules
Generates custom design system rules for the user's codebase. Use when user says "create design system rules", "generate rules for my project", "set up design rules", "customize design system guidelines", or wants to establish project-specific conventions for Figma-to-code workflows. Requires Figma MCP server connection.
figma-create-new-file
Create a new blank Figma file. Use when the user wants to create a new Figma design or FigJam file, or when you need a new file before calling use_figma. Handles plan resolution via whoami if needed. Usage — /figma-create-new-file [editorType] [fileName] (e.g. /figma-create-new-file figjam My Whiteboard)
aspnet-core
Build, review, refactor, or architect ASP.NET Core web applications using current official guidance for .NET web development. Use when working on Blazor Web Apps, Razor Pages, MVC, Minimal APIs, controller-based Web APIs, SignalR, gRPC, middleware, dependency injection, configuration, authentication, authorization, testing, performance, deployment, or ASP.NET Core upgrades.
notion-spec-to-implementation
Turn Notion specs into implementation plans, tasks, and progress tracking; use when implementing PRDs/feature specs and creating Notion plans + tasks from them.
openai-docs
Use when the user asks how to build with OpenAI products or APIs and needs up-to-date official documentation with citations, help choosing the latest model for a use case, or explicit GPT-5.4 upgrade and prompt-upgrade guidance; prioritize OpenAI docs MCP tools, use bundled references only as helper context, and restrict any fallback browsing to official OpenAI domains.
Use when tasks involve reading, creating, or reviewing PDF files where rendering and layout matter; prefer visual checks by rendering pages (Poppler) and use Python tools such as `reportlab`, `pdfplumber`, and `pypdf` for generation and extraction.
playwright-interactive
Persistent browser and Electron interaction through `js_repl` for fast iterative UI debugging.
playwright
Use when the task requires automating a real browser from the terminal (navigation, form filling, snapshots, screenshots, data extraction, UI-flow debugging) via `playwright-cli` or the bundled wrapper script.
render-deploy
Deploy applications to Render by analyzing codebases, generating render.yaml Blueprints, and providing Dashboard deeplinks. Use when the user wants to deploy, host, publish, or set up their application on Render's cloud platform.
cloudflare-deploy
Deploy applications and infrastructure to Cloudflare using Workers, Pages, and related platform services. Use when the user asks to deploy, host, publish, or set up a project on Cloudflare.
develop-web-game
Use when Codex is building or iterating on a web game (HTML/JS) and needs a reliable development + testing loop: implement small changes, run a Playwright-based test script with short input bursts and intentional pauses, inspect screenshots/text, and review console errors with render_game_to_text.
doc
Use when the task involves reading, creating, or editing `.docx` documents, especially when formatting or layout fidelity matters; prefer `python-docx` plus the bundled `scripts/render_docx.py` for visual checks.
chatgpt-apps
Build, scaffold, refactor, and troubleshoot ChatGPT Apps SDK applications that combine an MCP server and widget UI. Use when Codex needs to design tools, register UI resources, wire the MCP Apps bridge or ChatGPT compatibility APIs, apply Apps SDK metadata or CSP or domain settings, or produce a docs-aligned project scaffold. Prefer a docs-first workflow by invoking the openai-docs skill or OpenAI developer docs MCP tools before generating code.
spreadsheet
Use when tasks involve creating, editing, analyzing, or formatting spreadsheets (`.xlsx`, `.csv`, `.tsv`) with formula-aware workflows, cached recalculation, and visual review.
sora
Use when the user asks to generate, edit, extend, poll, list, download, or delete Sora videos, create reusable non-human Sora character references, or run local multi-video queues via the bundled CLI (`scripts/sora.py`); includes requests like: (i) generate AI video, (ii) edit this Sora clip, (iii) extend this video, (iv) create a character reference, (v) download video/thumbnail/spritesheet, and (vi) Sora batch planning; requires `OPENAI_API_KEY` and Sora API access.
speech
Use when the user asks for text-to-speech narration or voiceover, accessibility reads, audio prompts, or batch speech generation via the OpenAI Audio API; run the bundled CLI (`scripts/text_to_speech.py`) with built-in voices and require `OPENAI_API_KEY` for live calls. Custom voice creation is out of scope.
slides
Create and edit presentation slide decks (`.pptx`) with PptxGenJS, bundled layout helpers, and render/validation utilities. Use when tasks involve building a new PowerPoint deck, recreating slides from screenshots/PDFs/reference decks, modifying slide content while preserving editable output, adding charts/diagrams/visuals, or diagnosing layout issues such as overflow, overlaps, and font substitution.
sentry
Use when the user asks to inspect Sentry issues or events, summarize recent production errors, or pull basic Sentry health data via the Sentry API; perform read-only queries with the bundled script and require `SENTRY_AUTH_TOKEN`.
transcribe
Transcribe audio files to text with optional diarization and known-speaker hints. Use when a user asks to transcribe speech from audio/video, extract text from recordings, or label speakers in interviews or meetings.
winui-app
Bootstrap, develop, and design modern WinUI 3 desktop applications with C# and the Windows App SDK using official Microsoft guidance, WinUI Gallery patterns, Windows App SDK samples, and CommunityToolkit components. Use when creating a brand new app, preparing a machine for WinUI, reviewing, refactoring, planning, troubleshooting, environment-checking, or setting up WinUI 3 XAML, controls, navigation, windowing, theming, accessibility, responsiveness, performance, deployment, or related Windows app design and development work.
yeet
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`).
skill-installer
Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos).
skill-creator
Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with specialized knowledge, workflows, or tool integrations.
vercel-deploy
Deploy applications and websites to Vercel. Use when the user requests deployment actions like "deploy my app", "deploy and give me the link", "push this live", or "create a preview deployment".
notion-meeting-intelligence
Prepare meeting materials with Notion context and Codex research; use when gathering context, drafting agendas/pre-reads, and tailoring materials to attendees.
netlify-deploy
Deploy web projects to Netlify using the Netlify CLI (`npx netlify`). Use when the user asks to deploy, host, publish, or link a site/repo on Netlify, including preview and production deploys.
linear
Manage issues, projects & team workflows in Linear. Use when the user wants to read, create or updates tickets in Linear.
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