bio-crispr-screens-batch-correction SKILL.md skillA
bio-crispr-screens-batch-correction from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-crispr-screens-batch-correction@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-crispr-screens-batch-correction/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 16,118 bytes
- Repository stars
- 662
- License
- MIT
Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility
Reference examples tested with: pyComBat 0.3.3+ (epigenelabs/pyComBat), MAGeCK 0.5.9+, R/limma 3.58+, sva 3.50+, RUVSeq 1.36+, pandas 2.2+, numpy 1.26+, scikit-learn 1.4+, scipy 1.12+.
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show combat`; `from combat.pycombat import pycombat`
- R: `packageVersion('sva')`; `?ComBat`; `packageVersion('RUVSeq')`; `?RUVg`
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
## Batch Correction for CRISPR Screens
**"Correct batch effects in my CRISPR screens"** -> Diagnose the batch source, decide whether to remove via empirical-Bayes (ComBat), explicit covariate modeling (MAGeCK MLE / Chronos design matrix), control-guide-anchored normalization, or unwanted-variation decomposition (RUV, SVA), then apply only the correction that preserves biological condition signal.
- Python: `pyComBat.pycombat` for empirical-Bayes correction
- Python: explicit batch covariates in `mageck mle --design-matrix`
- R: `sva::ComBat`, `RUVSeq::RUVg`, `limma::removeBatchEffect`
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-crispr-screens-batch-correction@sha256:756e0483b7032f40The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_leyt2giputlfxvlx)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_leyt2giputlfxvlx GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-crispr-screens-batch-correction GET https://markdownregistry.com/api/v1/blob/756e0483b7032f403cb0f50e3a75299b2af134d2ed361b398b253122ebcaef37
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