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How to run trajectory analysis with only one cell type using palantir?

Hello,

I have single cell data that I have analyzed using scanpy and I have assigned the cell types to my clusters. I want to run palantir for trajectory analysis but only for the neutrophils in my data and I am not sure at which point I should filter my andata object for the neutrophils. Is it appropriate to do it like this?

  1. Import raw data again
  2. Do QC
  3. Normalize
  4. Log
  5. Filter for the neutrophils
  6. PCA
  7. Diffusion maps etc

Thank you

palantir scanpy
• 958 views • link
updated by npont • npont • written by bioinfo • bioinfo

Hello,

I was interested by the same topic. Did you follow this procedure at the end? I wonder if you should have filter for neutrophils and then normalize or indeed normalize before filtering for neutrophils. I am considering the first case for my analysis as follows: I have two datasets in which I filter for my cell type of interest and then I merge the datasets and I normalize.

Best

• 0 views • link
written by npont • npont

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