Experience with Cytobank

Question

[morten.hansen.01]

Dear all We are medical doctors and immunologists working with 16 color phenotype FCS files created on patient blood PBMC samples. We would like to independently work with a clustering algorithm that is intuitive and easy to manage. We have been exploring Cytobank briefly but we would like additional feedback. We know they are working on UMAP but so far offer FlowSOM, ViSNE and something called Citrus that analyze differences between several datasets e.g. responders vs nonresponders.

Any feedback would be helpfull,

Thanks in advance,

Morten Labmanager CCIT-DK Denmark

Answer 1

[jaro.slamecka]

I used to have access before setting up an R analysis pipeline and it seems like Cytobank is a pretty good option. It's fairly intuitive and documented well. They recently announced that they will be adding a "Dimensionality Reduction Suite" which will make it easier to compare algorithms and will include t-SNE-CUDA, UMAP and opt-SNE. But it did cost us around $2000 a year.

[morten.hansen.01]

Dear Jaro Thank you very much for your feedback. A single user-account seems to be currently priced a bit more but around what you have indicated. We have experienced that a good amount of our FCS fails to upload correctly but often succeds in second try. Additionally, we are still struggling with getting their advanced analysis to succeed but needs to get more into the workflow about adjusting parameters before the analysis.