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4 votes

Violin plots appear as vertical lines

I believe the reason is simply LTA and LTB not being expressed (or their expression not being detected due to technical limitations). If you would set the pt.size ...
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Does the number of RNA reads per cell obtained from the 10X scRNA experiment depend on amount of mRNA in given cell?

The number of reads per cell for any given experiment is largely technical. It depends on sequencing depth. 10X recommend 20K reads per cell for the v3 chemistry (and 50K reads per cell for v2)
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How will Seurat handle pre-normalized and pre-scaled data?

I notice that the paper points to the Broad website for data accession; have you looked there? https://singlecell.broadinstitute.org/single_cell/study/SCP1/-single-nucleus-rna-seq-of-cell-diversity-in-...
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Differentially expressed genes analysis in Seurat

@swbarnes2 code is one correct way to find marker genes that differ between samples. You could also change the Idents slot and then just use ...
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