Roy Granit, PhD comments

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                                            Roy Granit, PhD

Module request: CellRanger COUNT

+1 `metrics_summary.csv` provides the required info..

Module request: CellRanger COUNT

Hi Phil, I'll try and have a go at it.. 🤓

Module request: CellRanger COUNT

Hi @chris-rands, unfortunately have made much progress (beyond preparing my work ENV according to MultiQC spec).. hope to find some time in the next few weeks

Module request: CellRanger COUNT

I haven't gotten to read the multiqc documentation in order to implement the feature here, but wrote a simple package with some of this functionality.. https://github.com/compugen-ltd/supercells (sorry, it was just...

sc.pl.dotplot() `standard_scale='var'`: should scaling be changed?

@ivirshup @gokceneraslan any tutorial on how to apply z-score scaling or plans to add this feature in pl.dotplot? I believe this is the default with Seurat and it would be...

How to interpret negative log2 means in dot plot

Export styled dataframe to png not working with matplotlib

Docker on macOS arm64

Same issue here.. would be great to have a single image solution for mac and linux

Function to classify malignant/non-malignant cells

Yes, I believe your description of the function is correct. I've attempted to reproduce the plots that they generate using infercnvpy: ``` adata.obs["cnv_corr"] = 0 df=pd.DataFrame.sparse.from_spmatrix(adata.obsm['X_cnv']) adata.obs["cnv_corr"] = df.corrwith(df.mean(),axis=1).values ```...