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FlowCal
A library for reading, analyzing, and calibrating flow cytometry data. FlowCal can be run using an intuitive Microsoft Excel interface, or customizable Python scripts. The software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Additionally, FlowCal automatically gates data, calculates common statistics, and produces publication quality plots. FlowCal should ease the quantitative analysis of flow cytometry data within and across laboratories and facilitate the adoption of standard fluorescence units in synthetic biology and beyond.
flowFlowJo
Provides a way to extract data from one such commercial package, FlowJo, into the publicly accessible analysis platform R/Bioconductor. flowflowJo can produce R data structures with either summary statistics or fully flowCore compliant objects representing the various gates, compensation matrices, and other related information embedded in FlowJo sessions. Its goal is to make it easy to use compensation and gating information that has been produced using FlowJo. The flowFlowJo package provides the ability to work with both the raw data and the gating information in a powerful analysis environment that makes full use of the existing open source community efforts. Additional functionality is gained by the ability of the user to effectively run all of the compensation and gating functions described by the workspace(s) and automatically retrieve all of the relevant summary statistics into a concise data structure.
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