Markus Riester comments

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                                            Markus Riester

No off-target

Ill fix the deprecated warning for ggplot.

PureCN unintentionally filters out reads with supplementary alignments

Thanks so much @tinyheero. This code is indeed ancient and I'm not remembering why I implemented it that way. I will look into the impact. Gut feeling should not matter,...

PureCN unintentionally filters out reads with supplementary alignments

I'll go through my collections of normal and cancer test samples. If it's generally safe to add them even when normal samples do not, it probably makes indeed sense to...

SCTransform() Using All Cores

Running into the same issue, either I'm too stupid to tell `future` to only use 1 core or` SCTransform` is ignoring it. Does anybody got it to work?

Subscript out of bounds error during spatial integration in st_cluster.R

Hi, sorry I completely missed this one. I'm not sure, I think you would need to debug with ``` R --args --infile '/home/ngs/Desktop/ipmn_sctransform.list' --labels '/home/ngs/Desktop/ipmn_sctransform_labels.list' --outprefix /media/ngs/SSD/STTKIT/cluster/ipmn --gmt /home/ngs/Desktop/idep_cleaned.gmt --extra_gmt...