FlowKit Documentation

FlowKit is a Python toolkit for flow cytometry analysis and visualization, with full support for the GatingML 2.0 standard and limited support for FlowJo 10 workspace files.

FlowKit source

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• Index

• FlowKit API

• Tutorials
  • Basic Tutorial Series
    • FlowKit Tutorial - Part 1 - The Sample Class
    • FlowKit Tutorial - Part 2 - The transforms Module & Matrix Class
    • FlowKit Tutorial - Part 3 - The GatingStrategy & GatingResults Classes
    • FlowKit Tutorial - Part 4 - Programmatically creating a GatingStrategy using the gates Module
    • FlowKit Tutorial - Part 5 - The Session Class
    • FlowKit Tutorial - Part 6 - The Workspace Class
  • Advanced Examples
    • Clustering Comparison: Leiden vs Louvain
    • Dimension Reduction on Gated Populations
    • Compare Mean Fluorescence Intensity of Gated Events
    • Programmatically Replicate Gating from a FlowJo Workspace
    • Boolean Combinations of Gates
    • Saving Flow Analysis Data as AnnData objects for ScanPy
    • Apply scanpy to AnnData object