CyTOF gating tools
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
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