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markrobinsonuzh / cytofWorkflow

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FCS files with cluster labels #31

Closed juniajvs closed 11 months ago

juniajvs commented 12 months ago

Thank you so much for this amazing workflow!

We are currently having issues with some old-school immunologists that do not believe in the credibility of the clustering function done by flowSOM and CATALYST in your workflow and want to compare the data with their manual gating. Would it be possible to get FCS files with the cluster labels given by the workflow after using the cluster() function in the single cell experiment?

markrobinsonuzh commented 11 months ago

I haven't needed to do this in a very long time, but CATALYST does have this function:

https://rdrr.io/bioc/CATALYST/man/sce2fcs.html

.. so, it should be possible. It may require manual intervention for the cluster part though. For example, to get the cluster information into the data matrix of the FCS file, you might need to modify the sce2fcs steps.

Hope that helps, Mark