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A Robust BioConductor Framework for Automated Flow Data Analysis

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Commmand Line Tools

OpenCytoCL command line tools under development.

Paper published

The OpenCyto paper is has been published here.

The appropriate citation is:

Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, Kalams SA, De Rosa SC, Gottardo R. OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis. PLoS Comput Biol. 2014 Aug 28;10(8)

PubMed PMID: 25167361; PubMed Central PMCID: PMC4148203.

New features

The latest version of OpenCyto contains some changes to the way templates are written for cytokine or tailgate gates. We have moved the preprocessing for tailgate to be explicit. The collapseDataForGating should be set to FALSE and the preprocessing_method should be set to standardize_flowset, in order to get the same behavior as previously by default when collapseDataForGating was set to TRUE.

Getting Started

A good place to start is the package vignette.

Writing Plugins

More information on integrating your own gating functions is here


This is work in progress. Existing gating functions are documented here

Reproducible Examples

SDY207 (CyTOF data)

Gating of some CyTOF samples from study SDY207.

Analysis of the gated results form the CyTOF data.

HVTN080 (HIV Vaccine Clinical Trial Data)

Gating and extracting features

Visualization of gates

Analysis of pre- vs pos-vaccine in manual and OpenCyto analysis

Did you find a bug?

Please file a bug report! We count on you to let us know if something isn’t working as expected. Your feedback makes the software better for everyone.