AN
Data & Repro
AnnData
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Data & Repro
BU
bulk-rna-seq-batch-correction-with-combat
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-combat-correction
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- 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, w hich demonstrates the pyComBat workflow on ovarian cancer microarray cohorts.
- 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.
- 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.
Source Doc
Excerpt From SKILL.md
Examples
- "Combine three GEO ovarian cohorts, run ComBat, and export both the raw and corrected CSV matrices."
- "Plot PCA embeddings before and after batch correction to confirm that batches 1–3 overlap."
- "Save the harmonised AnnData file so I can reload it later for downstream DEG analysis."
Use cases
- Use bulk-rna-seq-batch-correction-with-combat for single-cell or spatial omics analysis.
- Apply bulk-rna-seq-batch-correction-with-combat 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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