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BI
bio-crispr-screens-batch-correction
Maintainer FreedomIntelligence · Last updated April 1, 2026
Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic technical variation.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-crispr-screens-batch-correction
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: scipy/sklearn for median normalization and batch correction.
- CLI: mageck test with batch-aware design.
- Correct batch effects in my CRISPR screens" → Normalize and harmonize sgRNA count data across screen batches to remove systematic technical variation while preserving biological signal. Python: scipy/sklearn for median normalization and batch correction CLI: mageck test with batch-aware design.
- Goal: Remove systematic library-size differences between batches.
- Approach: Scale each sample within a batch so that sample medians match a global median, correcting for sequencing depth variation.
Source Doc
Excerpt From SKILL.md
Batch Effect Removal with ComBat
Goal: Remove batch effects using empirical Bayes adjustment while preserving biological signal.
Approach: Log-transform counts, apply pyCombat with a batch vector, and back-transform to count space.
Batch QC Metrics
Goal: Quantify batch effect magnitude to determine whether correction is needed.
Approach: Run PCA on log-transformed counts, compute between-batch vs within-batch variance ratio, and assess whether batch structure dominates the first principal components.
Use cases
- Use when combining screens from multiple batches or correcting systematic technical variation.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- mageck-analysis - Batch-aware MAGeCK analysis
- screen-qc - Quality control before correction
- hit-calling - Analysis after batch correction
- library-design - Control guide design
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