x-cmd-network
This skill provides comprehensive network administration and diagnostic tools through x-cmd CLI, including network scanning with Nmap, ARP table management, DNS configuration, routing table analysis, and enhanced ping utilities. This skill should be used when users need to perform network diagnostics, troubleshoot connectivity issues, analyze network topology, or monitor network performance from command line interfaces.
x-cmd-git
This skill provides comprehensive Git and code hosting platform management tools through x-cmd CLI, including GitHub, GitLab, Codeberg, Forgejo integration, and Git hooks management. This skill should be used when users need to manage Git repositories, work with code hosting platforms, automate Git workflows, or configure Git hooks from command line interfaces.
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).
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.
spreadsheet
Use when tasks involve creating, editing, analyzing, or formatting spreadsheets (`.xlsx`, `.csv`, `.tsv`) using Python (`openpyxl`, `pandas`), especially when formulas, references, and formatting need to be preserved and verified.
linear
Manage issues, projects & team workflows in Linear. Use when the user wants to read, create or updates tickets in Linear.
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`).
sora
Use when the user asks to generate, remix, poll, list, download, or delete Sora videos via OpenAI’s video API using the bundled CLI (`scripts/sora.py`), including requests like “generate AI video,” “Sora,” “video remix,” “download video/thumbnail/spritesheet,” and batch video generation; requires `OPENAI_API_KEY` and Sora API access.
string-database
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
notion-knowledge-capture
Capture conversations and decisions into structured Notion pages; use when turning chats/notes into wiki entries, how-tos, decisions, or FAQs with proper linking.
imagegen
Use when the user asks to generate or edit images via the OpenAI Image API (for example: generate image, edit/inpaint/mask, background removal or replacement, transparent background, product shots, concept art, covers, or batch variants); run the bundled CLI (`scripts/image_gen.py`) and require `OPENAI_API_KEY` for live calls.
gh-fix-ci
Inspect GitHub PR checks with gh, pull failing GitHub Actions logs, summarize failure context, then create a fix plan and implement after user approval. Use when a user asks to debug or fix failing PR CI/CD checks on GitHub Actions and wants a plan + code changes; for external checks (e.g., Buildkite), only report the details URL and mark them out of scope.
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.
notion-research-documentation
Research across Notion and synthesize into structured documentation; use when gathering info from multiple Notion sources to produce briefs, comparisons, or reports with citations.
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.
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.
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.
gh-address-comments
Help address review/issue comments on the open GitHub PR for the current branch using gh CLI; verify gh auth first and prompt the user to authenticate if not logged in.
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.
ui-ux-pro-max
UI/UX design intelligence. 50 styles, 21 palettes, 50 font pairings, 20 charts, 9 stacks (React, Next.js, Vue, Svelte, SwiftUI, React Native, Flutter, Tailwind, shadcn/ui). Actions: plan, build, create, design, implement, review, fix, improve, optimize, enhance, refactor, check UI/UX code. Projects: website, landing page, dashboard, admin panel, e-commerce, SaaS, portfolio, blog, mobile app, .html, .tsx, .vue, .svelte. Elements: button, modal, navbar, sidebar, card, table, form, chart. Styles: glassmorphism, claymorphism, minimalism, brutalism, neumorphism, bento grid, dark mode, responsive, skeuomorphism, flat design. Topics: color palette, accessibility, animation, layout, typography, font pairing, spacing, hover, shadow, gradient. Integrations: shadcn/ui MCP for component search and examples.
zinc-database
Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
zarr-python
Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
venue-templates
Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.
vaex
Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that do not fit in memory.
uspto-database
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
uniprot-database
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
umap-learn
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
treatment-plans
Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.
transformers
This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
torch-geometric
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
torchdrug
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.
statsmodels
Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided statistical test selection with APA reporting use statistical-analysis.
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.
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.
stable-baselines3
Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent systems, or custom vectorized environments, use pufferlib instead.
statistical-analysis
Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use statsmodels.
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.
research-lookup
Look up current research information using Perplexity Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations.
rowan
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.
scanpy
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
scholar-evaluation
Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.
scientific-brainstorming
Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.
scientific-critical-thinking
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
scientific-schematics
Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
scientific-slides
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
scientific-visualization
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
scientific-writing
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
scikit-learn
Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
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