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nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
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Resurrect CytoSPADE for the poor #135

Open FrejaVenning opened 7 years ago

FrejaVenning commented 7 years ago

Hi,

I am new to SPADE and have tried the Cytobank version of it and really liked it, but I cannot afford a premium subscription :(

FlowJo, which my department does supply me with, has just incorportated SPADE through R, and it is working well for me - except that FlowJo offers no way of dynamically visualizing the SPADE-trees.... no annotations or anything. So, I wanted to try the SPADE CytoSCAPE plugin and use the v.2.8.2 of CytoSCAPE to visualize and annotate my trees. But I haven't managed so far.

Is there any way I can still get this new version of SPADE to talk to CytoSCAPE? Through R or by creating/installing the SPADE plugin for the older version of CytoSCAPE?

SamGG commented 7 years ago

Hi, Did you try Matlab SPADE 3.0 as an alternative? http://pengqiu.gatech.edu/software/SPADE/ I think Matlab is no more needed. Let us know. Take a look at ViSNE, Wanderlust, PhenoGraph, Wishbone https://www.c2b2.columbia.edu/danapeerlab/html/cyt-download.html Best.

zbjornson commented 7 years ago

Hej! I understand and apologize that it's no longer working. Resurrecting the Cytoscape plugin is unfortunately not feasible because it only works with a long-defunct version of Cytoscape that, if I recall, cannot be installed easily. Sometime I would like to make a separate viewer, but have no timeline for that. SamGG's suggestion is worth looking into -- will that address your needs?

dm319 commented 7 years ago

love the title! I second Sam's suggestion - though disappointed the standalone doesn't run in linux. isn't visne just tsne? will have to check out wanderlust and wishbone...

esimonds commented 7 years ago

Let me reiterate our apology that there is no longer a free SPADE GUI from the Nolan lab. On the bright side, there are several new tools out there (besides those in Premium Cytobank), some of which have already been mentioned:

SPADE 3.0 (does NOT require a full Matlab installation) http://pengqiu.gatech.edu/software/SPADE/

Cyt (includes viSNE, Wanderlust, PhenoGraph, Wishbone) (DOES require a full Matlab installation) https://www.c2b2.columbia.edu/danapeerlab/html/cyt-download.html

SCAFFOLD: https://github.com/nolanlab/scaffold https://www.ncbi.nlm.nih.gov/pubmed/26160952

X-Shift: https://github.com/nolanlab/vortex/releases https://www.ncbi.nlm.nih.gov/pubmed/27183440

Cytofkit (includes a GUI for running viSNE and PhenoGraph): https://github.com/JinmiaoChenLab/cytofkit http://journals.plos.org/ploscompbiol/article?id=10. 1371/journal.pcbi.1005112

On Fri, Mar 24, 2017 at 3:46 PM, dm319 notifications@github.com wrote:

love the title! I second Sam's suggestion - though disappointed the standalone doesn't run in linux. isn't visne just tsne? will have to check out wanderlust and wishbone...

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SamGG commented 7 years ago

Thanks Erin.

FrejaVenning commented 7 years ago

Thank you for all the prompt replies :)

I had just found SPADE 3.0 myself and an going to test it now, the cytofkit is pretty cool too, and I will also check out the other tools!

Thanks again!