Metadata-Version: 2.1
Name: FlowKit
Version: 0.1.0
Summary: Flow Cytometry Toolkit
Home-page: https://github.com/whitews/flowkit
Author: Scott White
License: BSD
Description: # <img alt="FlowKit" src="flowkit/resources/flowkit.png" />
        
        [![PyPI license](https://img.shields.io/pypi/l/flowkit.svg?colorB=dodgerblue)](https://pypi.python.org/pypi/flowkit/)
        [![PyPI version](https://img.shields.io/pypi/v/flowkit.svg?colorB=blue)](https://pypi.python.org/pypi/flowkit/)
        [![Build Status](https://travis-ci.com/whitews/FlowKit.svg?branch=master)](https://travis-ci.com/whitews/FlowKit)
        
        ## Overview
        
        FlowKit is an intuitive Python toolkit for flow cytometry analysis and visualization, including GatingML 2.0 support. Features include:
        
        * Reading Flow Cytometry Standard data (FCS files), including FCS versions:
          * 2.0
          * 3.0
          * 3.1
        * Exporting FCS data in any of the following formats:
          * A new FCS 3.1 file, with modified metadata and/or filtered events
          * NumPy array
          * Pandas DataFrame
          * CSV text file
        * Compensating FCS events using spillover matrices in multiple formats:
          * As the $SPILL or $SPILLOVER keyword value format
          * FlowJo tab-delimited text format
          * NumPy array
          * GatingML 2.0 spectrumMatrix XML element
        * Tranformation of original or compensated events in a variety of transforms used in the flow community:
          * Logicle
          * Inverse hyperbolic sine (arcsinh)
          * Hyperlog
          * Logarithmic
          * Channel ratios
          * Linear
        * Optional, automatic filtering of negative scatter events and/or anomalous events
        * Visualizing FCS event data:
          * Histogram of single channel data with a Gaussian kernel density estimate curve
          * Contour density plot of two channels
          * Interactive scatter plot of two channels
          * Interactive scatter plot matrix of any combination of channels
        
        <img alt="Screenshot of scatterplot" src="examples/fk_scatterplot.png" style="width:200px;" />
        
        ## Requirements
        
        FlowKit supports Python version 3.6 or above. All dependencies are installable 
        via pip, and include:
        
        * [flowio](https://github.com/whitews/flowio) >= 0.9.3
        * [flowutils](https://github.com/whitews/flowutils) >= 0.6.8
        * numpy >= 0.15
        * scipy >= 1.0
        * pandas >= 0.19
        * matplotlib >= 3.0
        * seaborn >= 0.9
        * bokeh >= 1.0
        * lxml >= 4.2
        * anytree >= 2.4
        
        ## Installation
        
        ### From PyPI
        
        `pip install flowkit`
        
        ### From source
        
        ```
        git clone https://github.com/whitews/flowkit
        cd flowkit
        python setup.py install
        ```
        
        ## Usage
        
        Check out the example notebooks:
        
        * [General Overview](https://github.com/whitews/FlowKit/blob/master/examples/flowkit-tutorial.ipynb)
        * [Applying Transforms to a Sample](https://github.com/whitews/FlowKit/blob/master/examples/sample_transforms.ipynb)
Platform: UNKNOWN
Description-Content-Type: text/markdown
