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Want to get involved in the development of FlowKit? Comparison between Leiden & Louvain clustering.Dimension reduction on gated populations.Importing a FlowJo 10 WSP file & replicating analysis in FlowKit.Customize gate for a single Sample in a Session sample group.Compare mean fluorescence intensity (MFI) in gated populations.If you have an example you would like to submit for consideration in this list (preferably with data), please submit an issue. Part 3 - GatingStrategy & GatingResults ClassesР”В«elow are more advanced and practical examples for using FlowKit.Part 2 - transforms Module & Matrix Class.

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Clone the repo (or download the example notebooks), and run them locally to see the fully interactive plots. Note, the interactive scatterplots do not render on GitHub.

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The series of Jupyter notebook tutorials can be found in the examples directory of this repository. If you have any questions about FlowKit, find any bugs, or feel something is missing from the tutorials below please submit an issue to the GitHub repository here. The tutorial notebooks in the examples directory are a great place to get started with FlowKit, and are linked below. The FlowKit API documentation is available on ReadTheDocs here. Note: FlowKit and FlowUtils use C extensions for significant performanceР”Р„bove is required for correct Logicle and Hyperlog transformations.

Interactive scatter plots of gates with sample eventsР”Р‡lowKit supports Python version 3.6 or above.

Interactive scatter plot matrix of any combination of channels.

Interactive scatter plot of two channels.

Retrieve gating results as a Pandas DataFrame.

Programmatically create gating strategies including polygon, rectangle, range, ellipsoid, quadrant, and boolean gates.

Export a Session's sample group analysis as a FlowJo 10 workspace file.

Polygon, rectangle, ellipse, and quadrant gates.

Linear, logarithmic, bi-exponential, and logicle transforms.

Workspace files are currently limited to the following features:

Limited support for importing FlowJo 10 workspace files.

Export gating strategies as a valid GatingML XML document.

Import GatingML XML documents as gating strategies.

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Full support for the GatingML 2.0 specification.Create a compensation matrix from a set of compensation bead files.GatingML 2.0 spectrumMatrix XML element.Compensate events using spillover matrices from:.Read FCS files, supporting FCS versions 2.0, 3.0, and 3.1.Please submit an issue if you find any bugs related to this feature. Support is currently limited to exporting data from a single sample group. Version 0.6 added experimental support for exporting FlowJo 10 workspace files from a Session. FlowKit is an intuitive 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.

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