bio-crispr-screens-perturb-seq-analysis SKILL.md skillA
bio-crispr-screens-perturb-seq-analysis 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-perturb-seq-analysis@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
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skills/bioskills/bio-crispr-screens-perturb-seq-analysis/SKILL.md- Versions recorded
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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy…
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What the file says
## Version Compatibility
Reference examples tested with: Pertpy 0.6+, SCEPTRE 0.10+ (R / katsevich-lab/sceptre), Mixscape via Seurat 4.3+ or Pertpy, scanpy 1.10+, anndata 0.10+, pandas 2.2+, numpy 1.26+, scipy 1.12+.
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show pertpy scanpy anndata`
- R: `packageVersion('sceptre')`; `?sceptre`; `?Seurat::PrepLDA`
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
## Single-Cell Perturb-Seq Analysis
**"Analyze a single-cell pooled CRISPR perturbation screen"** -> Assign sgRNAs to cells, filter unperturbed escapers, normalize counts, fit per-gene differential expression conditioned on perturbation, and rank perturbations by their molecular effect.
- Python: `pertpy` unified framework for Mixscape + SCEPTRE-via-R + differential expression
- R: `sceptre` for low-MOI NB GLM + permutation testing
- Python/R: `Seurat::MixscapeLDA` and downstream
## Experimental Architecture Comparison
| Method | Year | Architecture | Readout | MOI | Single-cell sgRNA detection |
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How to install
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The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
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