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Citrus Download

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Posts: 55

Joined: Thu Jul 17, 2014 5:07 pm

Post Tue Dec 09, 2014 9:46 pm

Citrus Download

Hello All,

I have been hearing people talk about Citrus and after looking into this I think this would be a really great software for me to evaluate. When I try to load this package into R, though, it won't let me. Is there some kind of special permissions needed for this?

Also, what is the overall opinion on this software? Some say it is better than SPADE, but perhaps it's not as user friendly?




Posts: 4300

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Tue Dec 09, 2014 10:27 pm

Re: Citrus Download

Hi Chad,

I'll let others weigh in on the pluses and minuses of SPADE/Citrus/viSNE/ACCENSE/SWIFT/etc.

Citrus is meant to find significant differences between groups of samples. It does all the comparison, and you get out information on the clusters that are different. This sort of thing *is* what a lot of people want, so in that way it's great. But you need at least 2 groups to compare (ie, you can't run it on one file).

SPADE and ACCENSE, on the other hand, *do* give you information (like marker medians and fraction of all cells) about all the clusters (ACCENSE actually gives you an output file for all of the individual cell events, with a column that gives the cluster ID). But it's up to you to do additional analysis steps outside of the programs in order to find the differences between the samples. They can also be run on just one file.

You'll also get different numbers of clusters between each program due to the different algorithms. Some of this can be controlled by some user-specified thresholds (P value you're aiming for, number of target clusters, how many cells you're sampling if you're not using the entire file, etc). But some appears to be intrinsic to each program.


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