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hesselberthlab / scrunchy

R toolkit for the analysis of single-cell functional heterogeneity
https://scrunchy.hesselberthlab.org/
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pseudotime #3

Open jayhesselberth opened 5 years ago

jayhesselberth commented 5 years ago

Would pseudotime analysis be useful on functional data? Either alone or in combination with mRNA?

jayhesselberth commented 5 years ago

One analogy to pseudotime to consider are reaction dependencies in the functional data. For example, in the short and long patch BER pathway, there are several intermediates that are captured at each step, e.g.:

  1. incision
  2. nick translation
  3. flap endonuclease

Each of these different intermediates could be present at different levels in data from each cell, which may reflect activity of each of the required enzymes. So "pseudotime" here reflects a sort of experimental time course, where the accumulation of specific intermediates reflects the efficiency of each reaction.