single-cell-preprocessing-with-omicverse
Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-preprocessing --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 preprocessing with omicverse ## Overview Follow this skill when a user needs to reproduce the preprocessing workflow from the omicverse notebooks [`t_preprocess.ipynb`](../../omicverse_guide/docs/Tutorials-single/t_preprocess.ipynb), [`t_preprocess_cpu.ipynb`](../../omicverse_guide/docs/Tutorials-single/t_preprocess_cpu.ipynb), and [`t_preprocess_gpu.ipynb`](../../omicverse_guide/docs/Tutorials-single/t_preprocess_gpu.ipynb). The tutorials operate on the 10x PBMC3k dataset and cover QC filtering, normalisation, highly variable gene (HVG) detection, dimensionality reduction, and downstream embeddings. ## Instructions 1. **Set up the environment** - Import `omicverse as ov` and `scanpy as sc`, then call `ov.plot_set(font_path='Arial')` (or `ov.ov_plot_set()` in legacy notebooks) to standardise figure styling. - Encourage `%load_ext autoreload` and `%autoreload 2` when iterating inside notebooks so code edits propagate without restarting the kernel. 2. **Prepare input data** - Download the PBMC3k filtered matrix from 10x Genomics (`pbmc3k_filtered_gene_bc_matrices.tar.gz`) and extract it under `data/filtered_gene_bc_matrices/hg19/`. - Load the matrix via `sc.read_10x_mtx
- Overview
- Instructions
- Critical API Reference - Batch Column Handling
- Batch Column Validation - REQUIRED Before Batch Operations
- Common Batch-Related Pitfalls
- Highly Variable Genes (HVG) - Small Dataset Handling
- LOESS Failure with Small Batches
- Best Practices for Batch-Aware HVG
- Examples
- References
What does the single-cell-preprocessing-with-omicverse skill do?
Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-preprocessing --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.