cellcharter-local-optimized
CellCharter spatial transcriptomics analysis toolkit - complete documentation with precise file name-based categorization
cellcharter-local
CellCharter 本地离线文档 (Sphinx 构建), 从下载目录启动 HTTP 服务后抓取
cellchat-pkg-local-complete
CellChat 包源码随附的本地教程 + Rd 转换的函数文档 + R 源码 HTML - 完整覆盖173个文件
cellchat-pkg-local-fixed
CellChat cell-cell communication analysis toolkit - complete documentation with precise file name-based categorization
cellphonedb
Comprehensive skill for CellPhoneDB - Database of cell type markers and cell-cell communication analysis for single-cell data. Use for cell type annotation, ligand-receptor analysis, cell-cell interaction inference, and communication network visualization.
developing-heart-local-improved
Developing Heart Atlas - comprehensive cardiac development analysis with spatial multi-omics integration
developing-heart-local
Developing Heart Atlas notebooks converted to HTML (local)
envi-pkg-local-improved
ENVI spatial transcriptomics analysis toolkit - comprehensive documentation with tutorials and Python source code
envi-pkg-local
ENVI 本地文档+教程+源码 - 100%覆盖13个文件（Sphinx build + 手动转换 notebooks/py）
giottosuite-local
Giotto Suite 空间转录组学分析工具包 - 100%覆盖718个文件（37个教程+285个核心API+4个数据文档+344个扩展函数+49个工具函数）
liana-py-complete
Liana-py 细胞互作分析工具包 - 100%覆盖文档（60个核心文件+72个图片文件）
monocle3-truly-complete
Monocle3 单细胞轨迹分析工具包 - 100%覆盖文档（18个文件：完整教程+API+轨迹推断）
mudata-complete
MuData 多模态数据分析工具包 - 100%覆盖文档（API+教程+IO指南+核心功能）
nichecompass-docs-local
NicheCompass 本地文档（en/latest）
organ-axis-complete
Organ Axis tutorial docs - 100%覆盖文档（模型应用+公式+注释采样+教程)
osta-docs-local
OSTA 本地文档（OSTA/）
palantir-docs-local
Palantir 本地文档（en/latest）
rapids-singlecell-complete
RAPIDS Single-Cell GPU 文档完整镜像
remote-server-executor
Remote SSH server management and code execution with paramiko-based performance optimization
sc-best-practices-complete-100percent
单细胞分析最佳实践集合 - 100%完整覆盖（410个文件：407个HTML文档+3个项目文档）
scanpy-complete
Scanpy 单细胞分析工具包 - 100%覆盖文档（API+教程+预处理+分析+可视化）
scanpy-single-cell-analysis
Python-based single cell analysis using Scanpy for .h5ad files in conda scanpy environment
scarches-complete
scArches 单细胞深度学习参考图谱框架 - 100%覆盖文档（26个HTML文件，包含完整API、教程、模型训练、多模态整合）
scarches-docs-complete
scArches 文档本地镜像全量
scarches
Comprehensive skill for scARCHES - Deep learning library for single-cell analysis of chromatin accessibility data. Use for scATAC-seq data processing, model training, batch correction, integration with scRNA-seq, and spatial chromatin analysis.
scglue-complete
scGLUE 单细胞多组学数据整合工具包 - 100%覆盖文档（完整API+教程+数据整合+图谱分析）
scvelo-complete
scVelo RNA速度分析工具包 - 100%覆盖文档（78个文件：完整API+教程+动态建模+可视化）
scvitools-complete
scvi-tools 单细胞深度学习框架 - 100%覆盖文档（完整API+教程+模型训练+多模态整合）
scvitools-docs-truly-complete
scvi-tools 深度学习单细胞分析工具包 - 100%覆盖文档（321个文件：完整API+用户指南+教程+开发者文档）
scvitools
Comprehensive skill for scvi-tools - Deep probabilistic models for single-cell omics analysis. Use for scVI, scANVI, totalVI, MultiVI models, single-cell RNA-seq integration, batch correction, differential expression, and multimodal data analysis.
seurat-local
Seurat 文档本地镜像（Satija Lab docs，包含 seurat/ 子目录与 archive）
seurat-single-cell-analysis
R-based single cell analysis using Seurat v5 for .rds/.rdata files
spata2-docs-local
SPATA2 空间转录组学分析工具包 - 100%覆盖414个核心文件（388个API参考+25个教程+1个主页）
spatialdata-docs-local
SpatialData 空间组学数据框架 - 100%覆盖271个核心文件（API文档+教程+示例+核心概念）
spatialdata-io-docs-local
SpatialData-IO 空间数据I/O工具包 - 100%覆盖85个核心文件（20个空间平台+6个API+6个CLI+53个生成器文档）
spatialdata
SpatialData framework for handling spatial multi-modal and multi-scale data. Use this skill for questions about spatial omics data analysis, visualization, and the SpatialData Python ecosystem.
test
HTML documentation test
xenium-benchmarking-docs-local
Xenium benchmarking 本地文档快照（全量 HTML）- 包含完整模块文档
github
GitHub CLI (gh) tool for retrieving and analyzing GitHub data including pull requests, issues, code search, workflow runs, releases, and repository information. Use when needing to read GitHub PRs, view comments, check CI/CD status, search code across repos, analyze issues, inspect action logs, or query any GitHub data. Focuses on information retrieval and analysis rather than modifications.
jira
Work with Jira issues using the jira CLI. Use for listing, creating, viewing, editing, deleting, cloning, and linking Jira issues. Supports CRUD operations, custom fields, JQL queries, epics, sprints, and common workflows like finding your assigned issues, filtering by status, and bulk operations.
apple-reminders
Access to Apple Reminders. PROACTIVELY USED when the user wants to see, add, complete, edit, move, or delete reminders or tasks. macOS only.
visualize-parsed-spatial-omics-metadata
Create an interactive HTML viewer to visualize and verify parsed metadata against source documents.
agent-memory
Persistent memory system for AI agents with semantic, episodic, and procedural memory types. Use when users want to (1) remember facts, preferences, or context across sessions, (2) track interaction history and experiences, (3) store reusable workflows or procedures, (4) build personalized agents that learn from conversations, or (5) implement any form of long-term memory for AI applications.
wow-moment-detector
Detects when a Claude Code session reaches a "wow moment" worth sharing with the team. A wow moment occurs during intensive back-and-forth discussions where both user and Claude deeply engage on a topic - repeatedly refining ideas, pushing back, questioning assumptions, and ultimately producing brilliant insights about effective human-AI collaboration. Triggers when the conversation shows signs of deep "cooking" - multiple sustained exchanges on the same topic, productive disagreements, or breakthrough moments emerging from persistent dialogue. This skill should stay alert throughout the session and invoke /show-ropes when a genuinely valuable agentic mindset insight emerges.
Excalidraw Generation
This skill should be used when the user asks to "create excalidraw diagram", "generate excalidraw", "hand-drawn diagram", "sketch diagram", "whiteboard style diagram", or when informal, spatial, annotated diagrams would best convey conceptual relationships. Expert in both presentation design AND artistic Excalidraw JSON creation.
LaTeX Handouts
This skill should be used when the user asks to "create LaTeX handout", "compile handout", "generate presentation handout", "create PDF document from slides", or needs guidance on LaTeX document structure, formatting, embedding images, or creating comprehensive presentation materials.
Presentation Design
This skill should be used when the user asks to "design a presentation", "structure presentation content", "improve presentation flow", "create presentation outline", "make slides more engaging", or needs guidance on storytelling, visual hierarchy, audience engagement, or presentation best practices.
Slide Quality Assessment
This skill should be used when the user asks to "analyze slide quality", "review slide", "check slide design", "optimize slide", "improve slide content", "assess slide clarity", or needs evidence-based quality evaluation using the 12-point checklist for presentation slides.
Slide Management
**MANDATORY USE - ALWAYS INVOKE THIS SKILL** when the user mentions ANY of these actions: "delete slide", "remove slide", "add slide", "insert slide", "create new slide", "new slide between", "get rid of slide", "fix gaps", "renumber slides", OR when they confirm/answer questions about slide deletion/addition (e.g., "yes delete slide 6", "add a slide after 5"). **CRITICAL - NEVER manually edit slides.md or rename slide files yourself** - this skill uses the manage-slides.py script which handles automatic renumbering, gap detection/fixing, git-aware operations, and slide number vs position conversion. **AUTO-TRIGGER IMMEDIATELY** when user wants to modify slide count, order, or numbering. This skill is the ONLY correct way to add/delete slides.
Slidev Mastery
This skill should be used when the user asks to "create slides with Slidev", "use Slidev syntax", "add Slidev components", "configure Slidev theme", "export Slidev presentation", or mentions Slidev-specific features like layouts, animations, Monaco editor, or code highlighting. Provides comprehensive Slidev expertise for markdown-based presentations.
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