AN
数据与复现
AnnData
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observ…
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数据与复现
SI
single-cell-clustering-and-batch-correction-with-omicverse
维护者 FreedomIntelligence · 最近更新 2026年4月1日
This skill distills the single-cell tutorials [`t_cluster.ipynb`](../../omicverse_guide/docs/Tutorials-single/t_cluster.ipynb) and [`t_single_batch.ipynb`](../../omicverse_guide/docs/Tutorials-single/t_single_batch.ipynb). Use it when a user wants to preprocess an `AnnData` object, explore clustering alternatives (Leiden, Louvain, scICE, GMM, topic/cNMF models), and evaluate or harmonise batches with omicverse utili….
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-clustering
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- This skill distills single-cell tutorials t_cluster.ipynb 、 t_single_batch.ipynb. Use it when user wants to preprocess AnnData object，explore 聚类 alternatives (Leiden，Louvain，scICE，GMM，topic/cNMF models)，、 evaluate 或 harmonise batches ，支持 omicverse utilities。
- Load omicverse as ov，scanpy as sc，、 plotting helpers (scvelo as scv when ，使用 dentate gyrus demo data)。
- Apply ov.plot_set() 或 ov.utils.ov_plot_set() so figures adopt omicverse styling before embedding plots。
- 用于 demo 聚类，fetch scv.数据集s.dentategyrus()；，用于 integration，read provided.h5ad files ，通过 ov.read() 、 set adata.obs['batch'] identifiers ，用于 each cohort。
- Confirm inputs are sparse numeric matrices；convert ，支持 adata.X = adata.X.astype(np.int64) when required ，用于 QC steps。
原始文档
SKILL.md 摘录
Examples
- "Normalise dentate gyrus cells, compare Leiden, scICE, and GMM clusters, and report ARI scores versus provided
clusters." - "Batch-correct three NeurIPS datasets with Harmony and scVI, produce MDE embeddings coloured by
batchandcell_type, and benchmark the embeddings." - "Fit topic and cNMF models on a preprocessed AnnData object, retrieve classifier-refined cluster calls, and visualise the resulting programs on UMAP."
适用场景
- Use single-cell-聚类-、-batch-correction-，支持-omicverse ，用于 single-cell 或 spatial omics analysis。
- Apply single-cell-聚类-、-batch-correction-，支持-omicverse to 聚类，integration，或 trajectory workflows。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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