Python tools for quantitative, reproducible flow cytometry analysis
Welcome to a different style of flow cytometry analysis. Take a look at some example Jupyter notebooks:
Packages such as FACSDiva and FlowJo are focused on primarily on identifying and counting subpopulations of cells in a multi-channel flow cytometry experiment. While this is important for many different applications, it reflects flow cytometry’s origins in separating mixtures of cells based on differential staining of their cell surface markers.
Cytometers can also be used to measure internal cell state, frequently as reported by fluorescent proteins such as GFP. In this context, they function in a manner similar to a high-powered plate-reader: instead of reporting the sum fluorescence of a population of cells, the cytometer shows you the distribution of the cells’ fluorescence. Thinking in terms of distributions, and how those distributions change as you vary an experimental variable, is something existing packages don’t handle gracefully.
A few things.
These are all in the setuptools spec.
For the core cytoflow library, you need the following Python packages:
python >= 2.7 pandas >= 0.19.2 numpy >= 1.9.0 numexpr >= 2.4.6 matplotlib >= 1.5.1 scipy >= 0.17 scikit-learn >= 0.18 seaborn >= 0.7.0 traits >= 4.6.0 nbformat >= 4.0 python-dateutil >= 2.5.2 statsmodels >= 0.8.0 fcsparser >= 0.1.1
For the GUI, you additionally need:
faulthandler >= 2.4 pyface == 5.1.0 envisage >= 4.5 pyqt >= 4.10 -- this must be installed separately!
Note that many of these packages have additional dependencies, including but not limited to traitsui, decorator, etc. Everything except PyQT should be a well well-behaved PyPI package; you should be able to install all the above with pip install or the Canopy package manager.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|File Name & Checksum SHA256 Checksum Help||Version||File Type||Upload Date|
|cytoflow-0.5.2-cp27-cp27m-macosx_10_7_x86_64.whl (427.0 kB) Copy SHA256 Checksum SHA256||cp27||Wheel||May 21, 2017|
|cytoflow-0.5.2-cp27-cp27m-win32.whl (416.3 kB) Copy SHA256 Checksum SHA256||2.7||Wheel||May 21, 2017|
|cytoflow-0.5.2-cp27-cp27m-win_amd64.whl (420.3 kB) Copy SHA256 Checksum SHA256||2.7||Wheel||May 21, 2017|
|cytoflow-0.5.2.tar.gz (5.3 MB) Copy SHA256 Checksum SHA256||–||Source||May 21, 2017|
|cytoflow-0.5.2.win32-py2.7.exe (685.7 kB) Copy SHA256 Checksum SHA256||2.7||Windows Installer||May 21, 2017|
|cytoflow-0.5.2.win-amd64-py2.7.exe (723.0 kB) Copy SHA256 Checksum SHA256||2.7||Windows Installer||May 21, 2017|