Usage with integrated data?
hummuscience opened this issue · comments
I was wondering if it is possible to use your package with embedding (integrated data), such as the output from Harmony.
If yes, could you explain how?
I think so. You can extract integrated data from Harmony as input data for SCMarker.
Harmony does not generate corrected counts, only a corrected embedding (PCA) that can be used for clustering.
SCMarker selects gene feature to help clustering instead of PCA feature. It can't be applied on PCA data.
Thank you for the information :) This answers my question