bio-single-cell-perturb-seq
Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function through pooled genetic perturbations in single cells.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-perturb-seq --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: MAGeCK 0.5+, pandas 2.2+, pertpy 0.7+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Perturb-seq Analysis **"Analyze my Perturb-seq CRISPR screen"** → Link guide RNA assignments to transcriptional phenotypes in pooled CRISPR screens with single-cell readout to identify gene function. - Python: `pertpy.tl.Mixscape(adata)` for perturbation classification, `pertpy.tl.Augur` for prioritization ## Load and Annotate Perturbations ```python import scanpy as sc import pertpy as pt adata = sc.read_h5ad('perturb_seq.h5ad') # Guide assignments typically stored in obs # Format: cell barcode -> guide identity -> target gene adata.obs['guide_id'] = guide_assignments['guide_id'] adata.obs['target_gene'] = guide_assignments['target_gene'] # Mark non-targeting controls adata.obs['is_con
- Version Compatibility
- Load and Annotate Perturbations
- Pertpy Analysis
- Perturbation Embedding
- Mixscape (Seurat v5)
- Mixscape Visualization
- Guide Assignment from CRISPR Feature Barcode
- Guide Quality Control
- Multi-Guide Analysis
- Pseudobulk Differential Expression
- Pathway Enrichment
- Screen QC Metrics
- Related Skills
What does the bio-single-cell-perturb-seq skill do?
Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function through pooled genetic perturbations in single cells.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-perturb-seq --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.