Software

Bioconductor software packages

Open source Bioconductor packages for analysis of flow cytometry data provides a unified framework for bioinformaticians to develop methods to analyze and interpret flow cytometry data. The software packages relevant to flow cytometry include flowCore, flowViz, flowStats, flowQ, flowUtils, flowClust, flowFP, flowMeans, flowFlowJo and flowMerge.

Overview of software packages

flowWorkspace – provides functions to import flowJo workspaces into R.

ncdfFlow – provides

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netCDF backed access for BioConductor’s flow tools to support large flow cytometry data sets.

flowCore – handles importing, storing, preprocessing and assessment of data from flow cytometry experiments.

flowViz – provides graphical methods for visualization of flow cytometry data.
flowQ – provides quality control and quality assessment tools for

flow cytometry

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data.
flowStats – provides tools and methods to analyze flow cytometry data that is beyond the basic infrastructure provided in the flowCore package.
flowUtils – provides utilities, mainly to integrate foreign FCM analysis tools.
flowClust – implements mixture model based clustering algorithms for FCM data.
flowMerge – provides merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework.
flowMeans – identifies cell populations in flow cytometry data using non-parametric clustering and segmented-regression-based change point detection.
flowFP – fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and data mining tools for flow cytometry
flowFlowJo– provides tools to import workspaces created using FlowJo into R objects that can be directly used in flowCore.
plateCore – statistical tools and data structures for plate based flow cytometry.

flowType – Phenotyping Flow Cytometry Assays using multidimentional expantion of single dimentional partitions.

SamSPECTRAL – Identifies Cell Populations in Flow Cytometry Data via Spectral Clustering