sc-best-practices-auto
单细胞分析最佳实践集合——目录索引自动发现，完整抓取HTML/MD与代码块
archr-local
ArchR docs served from downloaded_docs/archr_scrape - comprehensive scATAC-seq analysis toolkit with all HTML files explicitly listed
banksy-merged-v3
BANKSY spatial transcriptomics analysis tool - complete documentation with notebooks and source code
banksy-merged-v4
BANKSY spatial transcriptomics analysis tool - complete documentation with precise file name-based categorization
banksy-merged
Combined Banksy notebooks and source code (deduplicated)
banksy
BANKSY spatial transcriptomics analysis - comprehensive documentation with notebooks and API
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.
crewai
When to use this skill: When you need help with CrewAI - building collaborative AI agents, crews, and workflows. Use for agent orchestration, task automation, multi-agent systems, flow management, and enterprise AI automation.
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