Individual skill
flow-cytometry-analysis
Complete flow cytometry analysis pipeline. FCS file handling, compensation, manual/automated gating, immunophenotyping, CFSE proliferation analysis, cell cycle analysis (Dean-Jett-Fox), and apoptosis assays. Extends flowio with analytical workflows. For raw FCS parsing only use flowio.
backend/cli/skills/biology/flow-cytometry-analysis/SKILL.md
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# Flow Cytometry Analysis: Complete Analysis Pipeline
## Overview
Flow Cytometry Analysis provides end-to-end computational workflows for analyzing flow cytometry data. Starting from FCS file parsing, through compensation matrix application, gating strategies (manual rectangular/polygon gates and automated Gaussian mixture model gating), to downstream analyses including immunophenotyping, CFSE proliferation tracking, cell cycle phase quantification (Dean-Jett-Fox model), and apoptosis assays (Annexin V/PI). This skill extends basic FCS file handling (flowio) with full analytical pipelines.
## When to Use This Skill
- Analyzing multi-color flow cytometry experiments
- Applying compensation matrices to correct spectral overlap
- Building sequential gating hierarchies (debris exclusion, singlet gating, live/dead, marker gating)
- Immunophenotyping with multi-marker panels (CD3, CD4, CD8, etc.)
- Quantifying cell proliferation from CFSE/CellTrace dilution
- Determining cell cycle phase distribution from DNA content histograms