ulcerative_colitis
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cssmillie
As a heads-up, I don't think the following works with the latest `Seurat`: ``` epi.seur = SetIdent(epi.seur, [email protected]$phenograph.k750) fib.seur = SetIdent(fib.seur, [email protected]$phenograph.k250) imm.seur = SetIdent(imm.seur, [email protected]$phenograph.k250) ``` I updated the...
Hi Chris, Thanks for the great paper and easy to follow analysis. I want to repeat this but using all healthy samples (not just the 10 in the training set)....
In run.r, lines 235-237, when creating covariance matrices, I believe one should convert the Sample column to factor (for epi.cov, fib.cov and imm.cov). This prevents p.find_markers in markers.r from throwing...
Hi, thanks for this great study. The link for the immune data is no more functioning... https://www.dropbox.com/sh/4t8p89kbw4miy8x/AAAogGRGtmgakzl3ApZzHrCsa?dl=0
Hello, I'd like to know how to draw a violin plot after filtering out the contaminated residues in the differential gene list. After the step of mast.all = mast.all [res...
Hi Christopher, we'd like to reproduce Fig 4C. What is each point overlaid on violins? - Average geneset x cell? therefore, the distribution's mean is the mean of the geneset?...
Dear Christopher, we were having some issues in reproducing the cell proportion plot in Figure 2a. It would be fantastic if you provided the script to generate it. Thank you,...
Hi, I am quite interested in the code relating to "Estimation of the droplet contamination rate and filtering of putative ambient RNA contaminants". When will you make the code public?...
Hi, I just saw the publication on Cell! Congratulation! I was wondering if you would mind sharing the code to public? Thanks Yuqi
