sanbomics_scripts

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Hi, Thank you for this tutorial! It is very useful and I have almost done. But I was trying to merge the data in the step: adata = scv.utils.merge(adata, ldata)....

xyin0918

I am curious why you are filtering the expression data to only include genes with a base mean over 50? I have not really seen this as a step in...

karenbobier

Hello, I loved the tutorial! I found this small bug when playing around with it: in the pp() when annotating mitochondrial genes: lowercase startswith("mt-") won't catch anything in this data...

ukmrs

Assigning mitocondrial genes variable

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In my dataset the mitocondrial genes are not all labeled with 'mt-', some of them are like 'NC_002333.23, NC_002333.24', for example. I have a txt file with all the mitocondrial...

mtrebelo

Hi, Hi, I was trying to follow the complete scRNA-seq tutorial using CellBender h5 out file, by changing adata = anndata_from_h5(mtx_path) (anndata_fromh5 being https://github.com/broadinstitute/CellBender/issues/57). When I train the solo model...

giorgiatosoni