bio-crispr-screens-batch-correction SKILL.md skillA
bio-crispr-screens-batch-correction from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-crispr-screens-batch-correction@git:20260927.7d8c90dPins git:20260927.7d8c90d in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/batch-correction/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260927.7d8c90d, committed Sep 27, 2026
- First version recorded
- Sep 13, 2026
- Size
- 15,884 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
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 fridrichmethod/awesome-skills/bio-crispr-screens-batch-correction@sha256:56ea7d8041b7da08The line at the top of this page pins the label git:20260927.7d8c90d, 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_ujh7w75kbpmjehxm)
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Versions
The registry has recorded 2 versions of this file, between Sep 13, 2026 and Sep 27, 2026, about one every 14 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260927.7d8c90d latest | 2026-09-27 | 7d8c90d | 15,884 B | A | view · diff |
| git:20260913.5d8c8f0 | 2026-09-13 | 5d8c8f0 | 22,646 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (15884 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ujh7w75kbpmjehxm GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-crispr-screens-batch-correction GET https://markdownregistry.com/api/v1/blob/56ea7d8041b7da08fdba2b2572bb959bc84c4a8d66658edb4b345674d63b12ec
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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