Example Strategies

This section covers example strategies utilizing and combining some of AliGaters more advanced gating functions to solve gating problems.

• Introduction
• Loading an example .fcs file
• Gating PBMCs using shortest path algorithms.
• Gating singlets using principal component based clustering
• Separating CD3 positives using local minima (valleySeek)
• Separating CD4 / CD8 using a quad gate
• Gating T-reg cells using density delimitation and bezier curves
• gating CD194 positives (valleySeek)
• T-helper subsets (valleySeek and densityDelimitation)
• CXCR5 positives (valleySeek and densityDelimitation)
• Follicular T-helper cells (densityDelimitation)
• Follicular T-helper subsets (quadGate)
• FMO based thresholds for HLA-DR positivity (gateThreshold)
• CD8 positive subsets (valleySeek and quadGate)
• Some more FMO based thresholds for HLA-DR positivity (gateThreshold)