scrublet
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swolock
Detect doublets in single-cell RNA-seq data
Hi, Thank you for developing Scrublet. I am using a combined pipeline from your and Wagner's repositories and had a question about the expected doublet rate to identify putative doublets....
Hi there, Thanks for a great tool! Can I use this tool to predict the data of scATAC?
Hi Stuart, The CellSystems paper, Default Preprocessing, notes that SVD was used in place of PCA for the Demuxlet example. Is there an option in the scrub_doublets or other function...
When doing from numpy.lib.arraypad import _validate_lengths I'm getting the following error: ``` --------------------------------------------------------------------------- ImportError Traceback (most recent call last) in ----> 1 from numpy.lib.arraypad import _validate_lengths ImportError: cannot import name...
Hi @swolock, thanks for this tool! It's blazing-fast and looks promising on the 10x PBMC data. However, when working on a larger dataset of T cells, the histograms don't have...
Building wheels for collected packages: annoy Building wheel for annoy (setup.py) ... error error: subprocess-exited-with-error × python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [14 lines...
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',...
Hello Scrublet team, I am trying to use Scrublet as a preprocessing step in my pipeline. I use a filtered anndata object with raw UMI counts. If I pass `normalize_variance...
Hi, I am really struggling to try and run scrublet on my h5 files from some 10X genomics data. I am a novice at any sort of coding and in...
Hi there, Is there any way that I can save the scrublet plots (scrub.plot_histogram() and scrub.plot_embedding()) to png or pdf file? Thanks! Best Dié
