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Analysis Software Platform

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Please be as geeky as possible. Reference, reference, reference.
Also, please note that this is a mixed bag of math-gurus and mathematically challenged, so choose your words wisely :-)
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fcl54643

Contributor

Posts: 21

Joined: Mon Nov 02, 2015 2:13 pm

Location: Greater Philadelphia Area

Post Wed Aug 16, 2017 6:11 pm

Analysis Software Platform

Hi everyone,

We have been using Cytobank for the past couple of years, however we are looking into other solutions to analyze our CyTOF data (mostly to cut down cost). I was wondering if any of you had experience using FlowJo with tSNE, SPADE and other Plugins. Any insight would be welcome.

Thank you,

Florence
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dimar94

Participant

Posts: 1

Joined: Mon Oct 30, 2017 4:48 pm

Post Mon Oct 30, 2017 5:21 pm

Re: Analysis Software Platform

Hi Florence,
Did you receive a response, I'm also looking for other cheaper options beside cytobank. Any help will be great.
Thank you!
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dtelad11

Master

Posts: 113

Joined: Mon Oct 31, 2016 6:26 pm

Post Tue Oct 31, 2017 3:18 pm

Re: Analysis Software Platform

FCS Express is another option. I have never used their software but based on discussion with their representative it is relatively cheap.

Random question, how many samples do you need to analyze?
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bc2zbUVA

Contributor

Posts: 22

Joined: Thu Nov 19, 2015 4:23 pm

Post Tue Oct 31, 2017 3:47 pm

Re: Analysis Software Platform

I've been building an analysis toolkit for high dimensional cytometry analysis if anyone wants to be a guinea pig. It relies on R and Bioconductor libraries, so you need to have those up and running for it to run properly. I've included brief instructions as to how to install those. At the moment, it will annotate your FCS files with flowSOM cluster numbers and minimum spanning tree coordinates. This means you will have three additional parameters (cytools_dim_x, cytools_dim_y, mapping) that will let you gate on those values as if they are regular channels. Both FlowJo and FCS express can use these annotated FCS files. AutoGate and OpenCyto are two free options that are tailored towards the traditional interface of cytometry data analysis. cyttools is "headless" and runs at the level of the command line. You don't get to see the data as it performs its analysis, nor is it set up to visualize the data after analysis. It is there purely to perform the high dimensional clustering. In the future, it will support flowType, MEM scores, and hypersphere based clustering. I am wrapping up the differential abundance and differential expression features, and they should be fully functional at the time of publication.

cyttools can be obtained via github here:

https://github.com/bc2zb/cyttools

AutoGate can be obtained here:

http://cytogenie.org/

OpenCyto (Also an R library) is covered in detail here:

http://opencyto.org/
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petterbrodin

Participant

Posts: 11

Joined: Thu Nov 28, 2013 7:32 am

Post Tue Oct 31, 2017 4:08 pm

Re: Analysis Software Platform

ACCENSE is a free, easy to use app for tSNE viz, gating on tSNE maps and some simple clustering. Definitively not a full pipeline, but some nice features. Free download here: www.cellaccense.com

Petter
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lrolsen

Participant

Posts: 4

Joined: Tue Oct 11, 2016 6:21 am

Post Tue Oct 31, 2017 6:27 pm

Re: Analysis Software Platform

I haven't tried it out yet, but for the GUI inclined, https://www.cytosplore.org/ seems neat. It's free for now, but not sure what their pricing will be like down the line.

Lars
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SeanBurke

Participant

Posts: 1

Joined: Tue Oct 31, 2017 4:06 pm

Post Tue Oct 31, 2017 6:33 pm

Re: Analysis Software Platform

I saw some comments coming through regarding FCS Express and thought I'd provide a link to some of information on tSNE. Please see https://www.denovosoftware.com/site/kb-tSNE.shtml for an overview of the tools in FCS Express, FAQ's, and a recorded webinar at the bottom of the page.

We also have tools for SPADE, PCA, kMeans, and can run R scripts from our interface. Keep in mind tSNE, SPADE, PCA, kMeans all run via our own user interface with no plugins or dependency on R so they are pretty simple to use.

You can always try these tools out for free via a demo from our website.

Sean Burke
Product Manager
De Novo Software

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