Flow Cytometry Toolkit
Project description
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
Requirements
FlowKit supports Python version 3.6 or above. All dependencies are installable via pip, and include:
- flowio >= 0.9.3
- 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:
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