Author: David Brann; Tatsuya Tsukahara; Caleb Weinreb; Darren W. Logan; Sandeep Robert Datta
Title: Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients Document date: 2020_3_27
ID: bb4h255w_38
Snippet: Cells with co-expression of male (Ddx3y, Eif2s3y, Kdm5d, and Uty) and female marker genes (Xist) were removed as potential doublets from the WOM dataset. For both datasets, doublet cell detection was performed per sample using DoubletFinder (62) and Scrublet (63) . Genes with at least 3 UMIs in at least 5 cells were used for downstream clustering and cell type identification. For the HBC lineage tracing dataset, the Bioconductor package scone was.....
Document: Cells with co-expression of male (Ddx3y, Eif2s3y, Kdm5d, and Uty) and female marker genes (Xist) were removed as potential doublets from the WOM dataset. For both datasets, doublet cell detection was performed per sample using DoubletFinder (62) and Scrublet (63) . Genes with at least 3 UMIs in at least 5 cells were used for downstream clustering and cell type identification. For the HBC lineage tracing dataset, the Bioconductor package scone was used to pick the top normalization ("none,fq,ruv_k=1,no_bio,batch"), corresponding to full quantile normalization, batch correction and removing one factor of unwanted variation using RUV (64) . A range of cluster labels were created by clustering using the partitioning around medoids (PAM) algorithm and hierarchical clustering in the clusterExperiment Bioconductor package author/funder. All rights reserved. No reuse allowed without permission.
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