role-creator
Create and update Codex custom agents using standalone custom-agent TOML files.
gemini-computer-use
Build and run Gemini 2.5 Computer Use browser-control agents with Playwright. Use when a user wants to automate web browser tasks via the Gemini Computer Use model, needs an agent loop (screenshot → function_call → action → function_response), or asks to integrate safety confirmation for risky UI actions.
Frontend Responsive Design Standards
Build responsive, mobile-first layouts using fluid containers, flexible units, media queries, and touch-friendly design that works across all screen sizes. Use this skill when creating or modifying UI layouts, responsive grids, breakpoint styles, mobile navigation, or any interface that needs to adapt to different screen sizes. Apply when working with responsive CSS, media queries, viewport settings, flexbox/grid layouts, mobile-first styling, breakpoint definitions (mobile, tablet, desktop), touch target sizing, relative units (rem, em, %), image optimization for different screens, or testing layouts across multiple devices. Use for any task involving multi-device support, responsive design patterns, or adaptive layouts.
frontend-design
Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, or applications. Generates creative, polished code that avoids generic AI aesthetics.
create-hook
Create or update Codex hooks for global or project scope by asking for scope and hook type when ambiguous, then writing the hook config, scripts, and any required feature flag config.
img-to-frontend
Use when the user wants an end-to-end premium visual design workflow for any type of website or web page created directly from images.
llm-council
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markdown-url
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openai-docs-skill
Query the OpenAI developer documentation via the OpenAI Docs MCP server using CLI (curl/jq). Use whenever a task involves the OpenAI API (Responses, Chat Completions, Realtime, etc.), OpenAI SDKs, ChatGPT Apps SDK, Codex, MCP integrations, endpoint schemas, parameters, limits, or migrations and you need up-to-date official guidance.
Agent Browser
A fast Rust-based headless browser automation CLI with Node.js fallback that enables AI agents to navigate, click, type, and snapshot pages via structured commands.
content-research-writer
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section. Transforms your writing process from solo effort to collaborative partnership.
llm-application-dev
Building applications with Large Language Models - prompt engineering, RAG patterns, and LLM integration. Use for AI-powered features, chatbots, or LLM-based automation.
video-downloader
Downloads videos from YouTube and other platforms for offline viewing, editing, or archival. Handles various formats and quality options.
backend-development
Backend API design, database architecture, microservices patterns, and test-driven development. Use for designing APIs, database schemas, or backend system architecture.
best-practices
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changelog-generator
Automatically creates user-facing changelogs from git commits by analyzing commit history, categorizing changes, and transforming technical commits into clear, customer-friendly release notes. Turns hours of manual changelog writing into minutes of automated generation.
ask-questions-if-underspecified
Clarify requirements before implementing. Do not use automatically, only when invoked explicitly.
lead-research-assistant
Identifies high-quality leads for your product or service by analyzing your business, searching for target companies, and providing actionable contact strategies. Perfect for sales, business development, and marketing professionals.
code-documentation
Writing effective code documentation - API docs, README files, inline comments, and technical guides. Use for documenting codebases, APIs, or writing developer guides.
job-application
Write tailored cover letters and job applications using your CV and preferred style
database-design
Database schema design, optimization, and migration patterns for PostgreSQL, MySQL, and NoSQL databases. Use for designing schemas, writing migrations, or optimizing queries.
browser-use
AI-driven browser automation via Model Context Protocol
data-transform
Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
tcga-bulk-data-preprocessing-with-omicverse
TCGA bulk RNA-seq preprocessing with pyTCGA: GDC sample sheets, expression archives, clinical metadata, Kaplan-Meier survival analysis, and annotated AnnData export.
spatial-transcriptomics-tutorials-with-omicverse
Spatial transcriptomics: Visium/HD, Stereo-seq, Slide-seq preprocessing (crop, rotate, cellpose), deconvolution (Tangram, cell2location, Starfysh), clustering (GraphST, STAGATE), integration, trajectory, communication.
single-trajectory-analysis
Trajectory & RNA velocity: PAGA, Palantir, VIA, dynamo, scVelo, latentvelo, graphvelo backends via ov.single.Velo. Pseudotime, stream plots.
single2spatial-spatial-mapping
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
scenic-gene-regulatory-network
SCENIC gene regulatory network: RegDiffusion GRN inference, cisTarget regulon pruning, AUCell scoring, RSS, regulon embeddings in OmicVerse.
single-cell-preprocessing-with-omicverse
Single-cell QC, normalization, HVG detection, PCA, neighbor graph, UMAP/tSNE embedding pipelines in OmicVerse (CPU/GPU).
single-popv-annotation
PopV population-level cell annotation: 10 algorithms (SCVI, SCANVI, CellTypist, OnClass, RF, SVM, XGBoost, BBKNN, HARMONY, SCANORAMA), consensus voting, pretrained hub models.
single-cell-multi-omics-integration
Multi-omics integration: MOFA factor analysis, GLUE unpaired alignment, SIMBA batch correction, TOSICA label transfer, StaVIA trajectory. Covers scRNA+scATAC paired/unpaired workflows.
single-cell-downstream-analysis
AUCell pathway scoring, metacell DEG, scDrug response, SCENIC regulons, cNMF programs, and NOCD community detection in OmicVerse.
single-cell-clustering-and-batch-correction-with-omicverse
Single-cell clustering (Leiden, Louvain, scICE, GMM), batch correction (Harmony, scVI, BBKNN, Combat), topic modeling, and cNMF in OmicVerse.
single-cell-cellphonedb-communication-mapping
CellPhoneDB v5 ligand-receptor analysis, CellChatViz plots, and the newer ccc_heatmap / ccc_network_plot / ccc_stat_plot communication visualizations in OmicVerse.
cellfate-pseudotime-gene-analysis
CellFateGenie: Adaptive Threshold Regression for pseudotime-associated gene discovery, Mellon density, lineage scoring via ov.single.Fate.
single-cell-annotation-skills-with-omicverse
Cell type annotation: SCSA, MetaTiME, CellVote consensus, CellMatch, GPTAnno, weighted KNN label transfer in OmicVerse.
omicverse-visualization-for-bulk-color-systems-and-single-cell-d
OmicVerse plotting: volcano, venn, boxplot, embedding, density, heatmap families, dotplot, convex hull, stacked bar, and Forbidden City color palettes.
gsea-enrichment-analysis
Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.
foundation-model-analysis
Foundation model workflows: scGPT, Geneformer, UCE, CellPLM cell embedding, annotation, integration via ov.fm unified API. 22 models.
fastq-analysis-pipeline
Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.
datasets-loading
OmicVerse built-in datasets: pbmc3k, pancreas, dentategyrus, zebrafish, immune, spatial, multiome, plus create_mock_dataset() and predefined_signatures GMT gene sets.
data-viz-plots
Publication-quality matplotlib/seaborn plots: scatter, heatmap, violin, bar, line, multi-panel figures. Works with ANY LLM provider.
data-stats-analysis
Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
data-io-loading
OmicVerse data I/O: use ov.read(), ov.io.read_h5ad, read_10x_h5, read_10x_mtx, read_visium, read_visium_hd, read_nanostring instead of scanpy. Covers h5ad, 10x, spatial, CSV formats.
data-export-pdf
Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
data-export-excel
Export analysis results, data tables, and formatted spreadsheets to Excel files using openpyxl. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
bulk-wgcna-analysis-with-omicverse
WGCNA co-expression network: soft-threshold, module detection, eigengenes, hub genes, and trait correlation in OmicVerse.
bulktrajblend-trajectory-interpolation
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.
bulk-rna-seq-deconvolution-with-bulk2single
Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-seq.
string-protein-interaction-analysis-with-omicverse
STRING protein-protein interaction network analysis with pyPPI: query STRING database, build PPI graphs, expand with add_nodes, and visualize styled networks for bulk gene lists.
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