bio-single-cell-doublet-detection
Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying and removing doublets from scRNA-seq data.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-doublet-detection --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: matplotlib 3.8+, numpy 1.26+, 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. # Doublet Detection Doublets are droplets containing two or more cells. They appear as artificial intermediate cell populations and must be removed before analysis. ## Scrublet (Python) **Goal:** Detect and score doublets in scRNA-seq data using simulated doublet profiles. **Approach:** Simulate artificial doublets by combining random cell pairs, embed real and simulated cells together, and score each cell's similarity to simulated doublets. **"Remove doublets from my data"** → Identify droplets containing multiple cells by comparing each cell's profile to computationally simulated doublets, then filter flagged cells. ### Basic Usage ```python import scrublet as scr import scanpy as sc import nump
- Version Compatibility
- Scrublet (Python)
- Basic Usage
- Adjust Parameters
- Visualize Doublet Scores
- Filter Doublets
- Set Manual Threshold
- DoubletFinder (R)
- With SCTransform
- Adjust Expected Doublet Rate
- scDblFinder (R/Bioconductor)
- From Seurat Object
- Multi-Sample Processing
- Expected Doublet Rates
What does the bio-single-cell-doublet-detection skill do?
Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying and removing doublets from scRNA-seq data.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-doublet-detection --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.