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"description": "# ![\"FlowKit\"](\"flowkit/resources/flowkit.png\")
\n\n[](https://pypi.python.org/pypi/flowkit/)\n[](https://pypi.python.org/pypi/flowkit/)\n[](https://travis-ci.com/whitews/FlowKit)\n\n## Overview\n\nFlowKit is an intuitive Python toolkit for flow cytometry analysis and visualization, including GatingML 2.0 support. Features include:\n\n* Reading Flow Cytometry Standard data (FCS files), including FCS versions:\n * 2.0\n * 3.0\n * 3.1\n* Exporting FCS data in any of the following formats:\n * A new FCS 3.1 file, with modified metadata and/or filtered events\n * NumPy array\n * Pandas DataFrame\n * CSV text file\n* Compensating FCS events using spillover matrices in multiple formats:\n * As the $SPILL or $SPILLOVER keyword value format\n * FlowJo tab-delimited text format\n * NumPy array\n * GatingML 2.0 spectrumMatrix XML element\n* Tranformation of original or compensated events in a variety of transforms used in the flow community:\n * Logicle\n * Inverse hyperbolic sine (arcsinh)\n * Hyperlog\n * Logarithmic\n * Channel ratios\n * Linear\n* Optional, automatic filtering of negative scatter events and/or anomalous events\n* Visualizing FCS event data:\n * Histogram of single channel data with a Gaussian kernel density estimate curve\n * Contour density plot of two channels\n * Interactive scatter plot of two channels\n * Interactive scatter plot matrix of any combination of channels\n\n![\"Screenshot](\"examples/fk_scatterplot.png\")
\n\n## Requirements\n\nFlowKit supports Python version 3.6 or above. All dependencies are installable \nvia pip, and include:\n\n* [flowio](https://github.com/whitews/flowio) >= 0.9.3\n* [flowutils](https://github.com/whitews/flowutils) >= 0.6.8\n* numpy >= 0.15\n* scipy >= 1.0\n* pandas >= 0.19\n* matplotlib >= 3.0\n* seaborn >= 0.9\n* bokeh >= 1.0\n* lxml >= 4.2\n* anytree >= 2.4\n\n## Installation\n\n### From PyPI\n\n`pip install flowkit`\n\n### From source\n\n```\ngit clone https://github.com/whitews/flowkit\ncd flowkit\npython setup.py install\n```\n\n## Usage\n\nCheck out the example notebooks:\n\n* [General Overview](https://github.com/whitews/FlowKit/blob/master/examples/flowkit-tutorial.ipynb)\n* [Applying Transforms to a Sample](https://github.com/whitews/FlowKit/blob/master/examples/sample_transforms.ipynb)\n\n",
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