scrublet
scrublet copied to clipboard
Doubets do not occupy distinct states
Code:
scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.05) #range is 0.05-0.1.
doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2,
min_cells=3,
min_gene_variability_pctl=85,
n_prin_comps=100, #set high since this is what I plan to use in Seurat
log_transform='TRUE')
scrub.set_embedding('UMAP', scr.get_umap(scrub.manifold_obs_, 10, min_dist=0.3))
scrub.plot_embedding('UMAP', order_points=True);
My histograms seem normal, but the umap indicates that I have A LOT of doublets in my sample - would this be expected?