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.
single-cell-preprocessing-with-omicverse
Single-cell QC, normalization, HVG detection, PCA, neighbor graph, UMAP/tSNE embedding pipelines in OmicVerse (CPU/GPU).
bulk-rna-seq-differential-expression-with-omicverse
Bulk RNA-seq DEG pipeline: gene ID mapping, DESeq2 normalization, statistical testing, volcano plots, and pathway enrichment in OmicVerse.
bulk-rna-seq-batch-correction-with-combat
Bulk RNA-seq batch correction with pyComBat: remove batch effects from merged cohorts, export corrected matrices, and benchmark visualizations.
biocontext-knowledge-queries
BioContext knowledge: UniProt, AlphaFold, STRING, Reactome, GO, PanglaoDB, PubMed, OpenTargets queries via ov.biocontext for gene annotation.
single-trajectory-analysis
Trajectory & RNA velocity: PAGA, Palantir, VIA, dynamo, scVelo, latentvelo, graphvelo backends via ov.single.Velo. Pseudotime, stream plots.
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.
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.
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.
single-cell-annotation-skills-with-omicverse
Cell type annotation: SCSA, MetaTiME, CellVote consensus, CellMatch, GPTAnno, weighted KNN label transfer in OmicVerse.
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.
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.
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-popv-annotation
PopV population-level cell annotation: 10 algorithms (SCVI, SCANVI, CellTypist, OnClass, RF, SVM, XGBoost, BBKNN, HARMONY, SCANORAMA), consensus voting, pretrained hub models.
vrm-mtoon-outline
Adjusting VRM MToon material outline thickness in three-vrm. Covers outline width modes, property access, and how to fix outlines that appear too thick when models are scaled.
webapp-testing
Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.
Vanilla JS UI Race Conditions (VRM vs Live2D)
Dealing with delayed DOM generation, lazy loading, and optimistic state synchronization in vanilla JavaScript without a reactive framework.
vrm-springbone-physics
Debugging and fixing VRM SpringBone physics issues in three-vrm, including hair/clothing physics that flies upward, sticks out horizontally, or behaves unnaturally.
tts-error-reporting
Convention for reporting errors from multiprocessing TTS workers to the main process frontend. Use this skill when modifying, adding, or debugging TTS workers in tts_client.py to ensure connection errors, quotas, and API limits correctly display Toast notifications to the user rather than failing silently.
gemini-openai-api
Gemini 模型通过 OpenAI 兼容 API 接入指南。包含：(1) 辅助 API 配置（summary/correction/emotion/vision），(2) extra_body 格式用于控制 thinking，(3) 响应格式处理（markdown 代码块）。当需要将 Gemini 作为辅助模型接入、配置 thinking 参数、或处理 Gemini API 返回格式时使用。
frontend-design
Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, artifacts, posters, or applications (examples include websites, landing pages, dashboards, React components, HTML/CSS layouts, or when styling/beautifying any web UI). Generates creative, polished code and UI design that avoids generic AI aesthetics.
ssr-hydration-scraping
Best practices for extracting data from modern React/Vue SSR pages (like Next.js or Nuxt.js) by targeting hydration state blocks (__NEXT_DATA__, __NUXT__) using regex and `jmespath`, avoiding brittle DOM selector scraping.
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 Claude's capabilities with specialized knowledge, workflows, or tool integrations.
pytest-asyncio-httpx-mocking
When masking httpx.AsyncClient with unittest.mock in Pytest, AsyncMock must be used instead of MagicMock for async methods like post/get to prevent TypeError when awaited.
push-to-pr
Push commits to an existing GitHub PR's source branch. NEVER create new branches. Use when the user says "push to PR #N", "push到PR", or any variation meaning to push local commits onto an existing pull request. Covers finding the PR's head branch via GitHub API, setting up the correct remote, and pushing with HEAD:<branch> syntax.
📝 任务完成后归档
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ammo-mmd-physics-hacks
应对 WebGL 端 MMD 物理 (Ammo.js) 炸模、穿模、卡顿等极限边缘工况的终极调优指南与 Hack 技巧。
3d-camera-interaction
Three.js 中处理 3D 模型拖拽、缩放、边界检测的正确方法。解决鼠标移动与模型移动不同步、缩放后只能看到模型一部分等问题。
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.
i18n
i18n (internationalization) toolkit for projects using i18next. Provides three main functions: (1) i18n-check - Detect hardcoded Chinese text in HTML/JS files, (2) i18n-fix - Replace hardcoded text with i18n markers, (3) i18n-sync - Align translation keys across multiple languages (zh-CN, en, ja, ko, zh-TW). Use when working on internationalization tasks, detecting untranslated strings, or syncing locale files.
🎨 UI 设计规范
Project N.E.K.O. 胶囊化 UI、品牌蓝视觉系统规范
mcp-builder
Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).
redis-js
Work with the Upstash Redis JavaScript/TypeScript SDK for serverless Redis operations. Use for caching, session storage, rate limiting, leaderboards, full-text search (querying, filtering, aggregating with @upstash/redis search extension), and all Redis data structures. Supports automatic serialization/deserialization of JavaScript types. Search also available via @upstash/search-redis and @upstash/search-ioredis adapters for TCP clients.
terraform-skill
Use when working with Terraform or OpenTofu - creating modules, writing tests (native test framework, Terratest), setting up CI/CD pipelines, reviewing configurations, choosing between testing approaches, debugging state issues, implementing security scanning (trivy, checkov), or making infrastructure-as-code architecture decisions
uv
Use `uv` instead of pip/python/venv. Run scripts with `uv run script.py`, add deps with `uv add`, use inline script metadata for standalone scripts.
openscad
Create and render OpenSCAD 3D models. Generate preview images from multiple angles, extract customizable parameters, validate syntax, and export STL files for 3D printing platforms like MakerWorld.
pi-share
Load and parse session transcripts from shittycodingagent.ai/buildwithpi.ai/buildwithpi.com (pi-share) URLs. Fetches gists, decodes embedded session data, and extracts conversation history.
sentry
Fetch and analyze Sentry issues, events, transactions, and logs. Helps agents debug errors, find root causes, and understand what happened at specific times.
tmux
Remote control tmux sessions for interactive CLIs (python, gdb, etc.) by sending keystrokes and scraping pane output.
update-changelog
Read this skill before updating changelogs
oebb-scotty
Austrian rail travel planner (ÖBB Scotty). Use when planning train journeys in Austria, checking departures/arrivals at stations, or looking for service disruptions. Covers ÖBB trains, S-Bahn, regional trains, and connections to neighboring countries.
web-browser
Allows to interact with web pages by performing actions such as clicking buttons, filling out forms, and navigating links. It works by remote controlling Google Chrome or Chromium browsers using the Chrome DevTools Protocol (CDP). When Claude needs to browse the web, it can use this skill to do so.
anachb
Austrian public transport (VOR AnachB) for all of Austria. Query real-time departures, search stations/stops, plan routes between locations, and check service disruptions. Use when asking about Austrian trains, buses, trams, metro (U-Bahn), or directions involving public transport in Austria.
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