bio-workflows-cytometry-pipeline
End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CATALYST/diffcyt. Use when processing flow or mass cytometry data end-to-end.
npx skills add BioTender-max/awesome-bio-agent-skills --skill cytometry-pipeline --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: FlowSOM 2.10+, edgeR 4.0+, flowCore 2.14+, ggplot2 3.5+, limma 3.58+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scikit-learn 1.4+ 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. # Flow Cytometry Pipeline **"Process my flow cytometry data from FCS to differential analysis"** → Orchestrate compensation, transformation, doublet removal, FlowSOM clustering, phenotype annotation, and diffcyt differential testing across conditions. ## Pipeline Overview ``` FCS Files ──> Compensation ──> Transformation ──> Gated/Clustered Data │ ▼ ┌─────────────────────────────────────────────────┐ │ cytometry-pipeline │ ├─────────────────────────────────────────────────┤ │ 1. Load FCS Files │ │ 2. Compensation & Transformation │ │ 3. QC & Filtering │ │ 4. Clustering (FlowSOM) or Gating │ │ 5. Dimensionality Red
- Version Compatibility
- Pipeline Overview
- Complete R Workflow (CATALYST)
- flowCore + Manual Gating Workflow
- Python Alternative (FlowCytometryTools)
- QC Checkpoints
- Workflow Variants
- CyTOF Data
- Paired Design
- Related Skills
What does the bio-workflows-cytometry-pipeline skill do?
End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CATALYST/diffcyt. Use when processing flow or mass cytometry data end-to-end.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill cytometry-pipeline --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.