bulk-rna-seq-batch-correction-with-combat
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-combat-correction --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.
# Bulk RNA-seq batch correction with ComBat ## Overview Apply this skill when a user has multiple bulk expression matrices measured across different batches and needs to harmonise them before downstream analysis. It follows [`t_bulk_combat.ipynb`](../../omicverse_guide/docs/Tutorials-bulk/t_bulk_combat.ipynb), w hich demonstrates the pyComBat workflow on ovarian cancer microarray cohorts. ## Instructions 1. **Import core libraries** - Load `omicverse as ov`, `anndata`, `pandas as pd`, and `matplotlib.pyplot as plt`. - Call `ov.ov_plot_set()` (aliased `ov.plot_set()` in some releases) to align figures with omicverse styling. 2. **Load each batch separately** - Read the prepared pickled matrices (or user-provided expression tables) with `pd.read_pickle(...)`/`pd.read_csv(...)`. - Transpose to gene × sample before wrapping them in `anndata.AnnData` objects so `adata.obs` stores sample metadata. - Assign a `batch` column for every cohort (`adata.obs['batch'] = '1'`, `'2'`, ...). Encourage descriptive labels when availa ble. 3. **Concatenate on shared genes** - Use `anndata.concat([adata1, adata2, adata3], merge='same')` to retain the intersection of genes across batches. - Confirm the
- Overview
- Instructions
- Examples
- References
What does the bulk-rna-seq-batch-correction-with-combat skill do?
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-combat-correction --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.