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single-cell-clustering-and-batch-correction-with-omicverse

Maintainer FreedomIntelligence · Last updated April 1, 2026

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….

OpenClawNanoClawAnalysisReproductionsingle-clustering🔬 omics & computational biologysingle-cell & spatial omicsguide

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-clustering

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • This skill distills the single-cell tutorials t_cluster.ipynb and 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 utilities.
  • Load omicverse as ov, scanpy as sc, and plotting helpers (scvelo as scv when using dentate gyrus demo data).
  • Apply ov.plot_set() or ov.utils.ov_plot_set() so figures adopt omicverse styling before embedding plots.
  • For demo clustering, fetch scv.datasets.dentategyrus(); for integration, read provided.h5ad files via ov.read() and set adata.obs['batch'] identifiers for each cohort.
  • Confirm inputs are sparse numeric matrices; convert with adata.X = adata.X.astype(np.int64) when required for QC steps.

Source Doc

Excerpt From SKILL.md

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 batch and cell_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."

Use cases

  • Use single-cell-clustering-and-batch-correction-with-omicverse for single-cell or spatial omics analysis.
  • Apply single-cell-clustering-and-batch-correction-with-omicverse to clustering, integration, or trajectory workflows.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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