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JonathanShor / DoubletDetection

Doublet detection in single-cell RNA-seq data.
https://doubletdetection.readthedocs.io/en/stable/
MIT License
81 stars 23 forks source link

List of barcode duplets #133

Closed ibseq closed 4 years ago

ibseq commented 4 years ago

hello, is there a way once we've ran dupeltdetection to have a list of these barcodes rather than only the umap plot?

thanks ibseq

adamgayoso commented 4 years ago

As stated on the readme, you can run

labels = clf.fit(raw_counts).predict() and labels is 1 if there is a doublet and 0 if not. np.nan are ambiguous cells. Labels will be in the same order as the cells in raw_counts, so you should be able to link labels to your barcodes.