CyTOForum

Hello everyone,

I was interested what software packages people prefer to use for basic gating of CyTOF data.

Previously we used Cytobank for initial gating to remove doublets, beads, Gaussian parameters and debarcoding before exporting the FCS files. Then we do the detailed analysis in R, mostly via the CATALYST package.
However it seems Cytobank have introduced a 1Gb limit on FCS file size that you can export events from. Since we normally handle large multiplexed files our current way of doing it often hits this limit.

So I was curious to know how everyone else prefers to do this, does this. Flowjo? Another R package?

Best,
James

Hi James,

There are many packages in R that can do this for you. Our personal favourite is the following paper (or parts of it):
https://www.sciencedirect.com/science/a ... 7021002130

Here is the GitHub link to the entire pipeline:
https://github.com/prybakowska/CyTOF_analysis_Pipeline1

There are packages written in Python as well that you could look into, e.g. I have used CytoFlow for the initial gating:
https://github.com/cytoflow/cytoflow

The following list from Bioconductor is quite comprehensive as well:
https://www.bioconductor.org/packages/r ... wCytometry

I hope this helps.

Good luck

Ratnadeep

Dear Ratnadeep,

Thanks a lot for your input. That does indeed help.
As you say some parts of that workflow look like they would fit what we are trying to do quite well.

Best,
James