Package: numpy-reduced-flowcytometrytools
Authors: Jonathan Friedman andEugene YurtsevFlowCytometryTools is a python package for visualization and analysis of high-throughput flow cytometry data.Intuitive: provides a simple programmatic interface to work with flow cytometry dataFlexible: can analyze either individual samples or collections of many platesScalable: simplifies analysis of high-throughput data using the power ofpandasWho is this for?FlowCytometryTools is for researchers who want to use the python programming language to analyze flow cytometry data.The package is specifically tailored for high-throughput analysis. It provides an interface that can directly work with collections of flow cytometry measurements (e.g., 96-well plates).Basic familiarity with the python programming languages is recommended.You can find a few example scripts that load and plot flow cytometry data in thegallerypage.If you like what you see, then proceed to theinstallationpage and then
to thetutorial.And yes, there’s a UI to draw basic gates. It’s super basic, but it gets the job done.FeaturesTransformations: hyperlog (hlog), truncated log (tlog), or anything you can dream of ;)Plotting: 1D, 2D histograms for both single samples and collections (e.g., 96-well plates).Gating: threshold, interval, quad, polygon gatesSubsampling: easy to subsample to examine only part of a measurement and randomize event orderGUI: simple graphical user interface to draw gates (wxorwebagg)FCS Formats: Supports FCS 2.0, 3.0, and 3.1ResourcesDocumentation:https://eyurtsev.github.io/FlowCytometryTools/Source Repository:https://github.com/eyurtsev/FlowCytometryToolsComments or questions:https://github.com/eyurtsev/FlowCytometryTools/issuesDependenciesFor more information about how to obtain these, please see theinstallationpage.FlowCytometryTools may work with older versions of some of these dependencies, but if
you run into issues, please update the dependencies.Required Dependenciespythonpython 2.7 or python 3pandas(Recommended version: 0.19.0 or higher).matplotlib(Recommended version: 1.5.3 or higher).scipyOptional Dependencieswx-python: Used for the FlowCytometryTools GUI.AlternativesFlowCytometryTools is not the only open source software for performing data analysis on flow cytometry data.So if you find that FlowCytometryTools does not suit your needs, take a look at the following software:cytoflow: API for python with a GUIfcm: API for pythonBioconductor: API for the R programming languageFlowPy: GUIcyflogic: GUIFlowing Software: GUIChangesv0.4.6, 2017-03-26FIX: edge case for inferring x-range for spline interpolation when doing log transforms and with data the contains values in the interval.FIX: fix linear transform (kwargs weren’t being passed correctly).FIX: interval gate was raising exceptions for certain numpy versions (fix by alonyan)v0.4.5, 2015-10-31Sample fcs files now included with installationMostly maintenance (tests, configuration files, etc.)v0.4.4, 2015-09-06** Repository moved to github **Enhancements:added an experimental web-based backend for drawing gates. Use FCMeasurement.view_inteactively(backend=’webagg’).col first enumerator for forming an ordered fcs file collection (Yoav Ram)Bug fixes:FCPlate.from_dir ID_kwargs match against full path, not just filename (Nick Bolten)fcs parser can read larger fcs files and handles blank headers (Ben Roth)v0.4.3, 2014-12-05ENHC: Automatically determine bin location when plotting plates.Fix for Accuri V6 FCS (Ben Roth)Fix for xlim/ylim when plotting 2d histogramsv0.4.2, 2014-10-08FCS parser can handle more formatsUpdated documentationv0.4.1, 2014-09-13Bug fixes for GUINow works with matplotlib 1.4.0Added documentation and examples to galleryv0.4.0, 2014-06-05Updates in documentationAdded experimental view() functionRenamed old view() function into -> view_interactively()Added queueing to help when dealing with large quantities of data.Histogram plots should work with pandas (0.14.0) & matplotlib (1.3.1).v0.3.6, 2014-02-11Mostly updates in documentationv0.3.5, 2014-01-19Boost in speed for transformations on collections of measurements (like 96-well plates).Much of the documentation has been updated and improved.Improved GUI.v0.3.0, 2013-10-27 Initial ReleaseLICENSEThe MIT License (MIT)Copyright (c) 2013-2015 Eugene Yurtsev and Jonathan FriedmanPermission is hereby granted, free of charge, to any person obtaining a copy
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