GitHub
cellchat-pkg-local-fixed
CellChat cell-cell communication analysis toolkit - complete documentation with precise file name-based categorization
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GitHub
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）
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GitHub
scanpy-single-cell-analysis
Python-based single cell analysis using Scanpy for .h5ad files in conda scanpy environment
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GitHub
seurat-single-cell-analysis
R-based single cell analysis using Seurat v5 for .rds/.rdata files
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GitHub
developing-heart-local-improved
Developing Heart Atlas - comprehensive cardiac development analysis with spatial multi-omics integration
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GitHub
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）
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GitHub
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
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GitHub
banksy-merged
Combined Banksy notebooks and source code (deduplicated)
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GitHub
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）
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GitHub
xenium-benchmarking-docs-local
Xenium benchmarking 本地文档快照（全量 HTML）- 包含完整模块文档
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GitHub
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 expr...
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GitHub
scarches-docs-complete
scArches 文档本地镜像全量
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GitHub
osta-docs-local
OSTA 本地文档（OSTA/）
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GitHub
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 infer...
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GitHub
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）
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GitHub
archr-local
ArchR docs served from downloaded_docs/archr_scrape - comprehensive scATAC-seq analysis toolkit with all HTML files explicitly listed
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GitHub
seurat-local
Seurat 文档本地镜像（Satija Lab docs，包含 seurat/ 子目录与 archive）
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GitHub
palantir-docs-local
Palantir 本地文档（en/latest）
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GitHub
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）
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GitHub
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）
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GitHub
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
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GitHub
rapids-singlecell-complete
RAPIDS Single-Cell GPU 文档完整镜像
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GitHub
developing-heart-local
Developing Heart Atlas notebooks converted to HTML (local)
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GitHub
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）
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