I know that many labs use either FlowJo or FCS Express to plot and analyze their flow data. These seem like the two standards for most labs (and I have used FlowJo before). However, my current funding does not cover software licenses and I'm not keen to pay $500-2000 out-of-pocket for a license.

Are there alternatives that approach the quality of FlowJo/FCS Express but are open-source/free with an academic license? I'm looking for an approach which will allow me to fit G1/S/G2-M curves to my data.

  • $\begingroup$ Meta-question on Meta: meta.biology.stackexchange.com/questions/743/… $\endgroup$
    – Luigi
    Commented Nov 20, 2014 at 0:48
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    $\begingroup$ Excel would do perfectly fine :) there are several plotting tools- R and Matlab have good plot tools. Get the text file out and plot anywhere you like. $500 is too much for that; just ridiculous. What you must know is how to analyze and what different parameters are— that you in any case must; you cant depend on a black box. $\endgroup$
    Commented Nov 20, 2014 at 8:24

2 Answers 2


Sounds like you should look into Bioconductor's flow suite. I actually really like doing flow analysis in R, but it takes some practice and getting used to.

The biggest problem you will run into (in my opinion) is gating. It's not easy to setup a GUI point and click gate. Rather, you'll be more forced and inclined to set limits with algorithms or hard value limits.

I found .Net Bio to be fun, but not nearly as powerful as Bioconductor.

Meta note, couldn't think of a less opinion oriented way to answer other than just to say "It can be done in R utilizing Bioconductor." If this is still off, I'm fine with deletion.


I created a free flow cytometry tool that works on any device https://www.redmatterapp.com/

The benefits of this tool is that it works on any device and analysis can be shared via a URL.

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    $\begingroup$ Hi Mark. Instead of simply posting a link to your tool, please provide some context and perhaps screen shots. Your answer should be able to stand on its own as being useful/informative without the need to visit other sites. A short one sentence answer with a link is likely to be deleted. Thanks. $\endgroup$ Commented Jun 21, 2017 at 18:26

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