GitHub
curate-genome-assembly
Process genome assembly datasets for VEuPathDB resources
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databases bioinformatics AI Skills
Discover databases bioinformatics skills, compare source repositories and read the instructions for each workflow.
Categories: databases bioinformatics
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GitHub
curate-bulk-rnaseq
Process bulk RNA-seq datasets for VEuPathDB resources
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GitHub
cellcharter-local-optimized
CellCharter spatial transcriptomics analysis toolkit - complete documentation with precise file name-based categorization
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GitHub
banksy-merged-v4
BANKSY spatial transcriptomics analysis tool - complete documentation with precise file name-based categorization
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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
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
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
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
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
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
rapids-singlecell-complete
RAPIDS Single-Cell GPU 文档完整镜像
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GitHub
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）
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GitHub
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）
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GitHub
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）
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GitHub
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）
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GitHub
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.
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GitHub
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-se...
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