This is an internal BIOFAB tool for flow cytometry data analysis.

It uses ellipsis or rectangular gating and clustering and outputs plots of the cluster distributions.
It outputs three types of data:

  An FCS file containing only the gated and filtered data.
  A plot showing the distribution of the clusters (one or two).
  A data file with the mean, variance, standard deviation and individual fluorescences.

We use this tool to analyze the data from our Millipore Guava easyCyte, and some of the code may be specific to the fcs files produced by this device.

Running using R directly:

  R --vanilla < test.r

Running using R through Ruby:

  ruby test.rb

Requirements:

  BioConductor libraries: flowCore, flowClust and flowViz
  For Ruby: rubygems, rsruby