single-cell-clustering-and-batch-correction-with-omicverse
Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_single_batch.ipynb.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-clustering --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Single-cell clustering and batch correction with omicverse ## Overview 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 utilities. ## Instructions 1. **Import libraries and set plotting defaults** - 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. 2. **Load data and annotate batches** - 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. 3. **Run quality control** - Execute `ov.pp.qc(adata, tresh={'mito_
- Overview
- Instructions
- Examples
- References
What does the single-cell-clustering-and-batch-correction-with-omicverse skill do?
Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_single_batch.ipynb.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-clustering --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.