Hi,
I am trying to analyse a scRNAseq dataset using the same parameters they have used, but I am struggling to understand how to implement the parameters for each function they have described in their methods.
How would I perform the following parameters with the functions?
sc.pp.neighbors function (parameters: n_neighbors = 50, n_pcs = 45, min_dist=0.3, adjusted ANN parameters of ntrees=200, search_k_factor=10)
Harmony integration in scanpy (parameters: theta=2.0, lambda=10, sigma=0.2)
They have also used the Scrublet package, but I am confused as to how to implement this.
I am new to scRNAseq analysis and would really appreciate any help or advice this forum can provide!
Thank you!