I have a large FACS project involving hundreds of files. So, it is not practical or suitable to manually gate these in Flowjo etc and to remove dead and duplicated cells. I have found many different methods and packages for cyTOF automation of these steps. I have yet to see any packages for FACS for these steps. I know there is a substantial difference in how you approach these two methodologies during the pre-processing steps. So I don't wish to use cyTOF packages.
Does anybody know of any packages that are useful for these steps? Or how to approach it from a novel standpoint.
Thanks in advance,