Gregor Sturm

Hi @Movahedilab, thanks for your report! I wasn't able to reproduce the error using `datasets.wu2020_3k()`, the indicated versions and your notebook. Since the input numbers of your notebook are not...

Hi Daliya, unfortunately GitHub discards attachments sent by email. Could you please upload them using the web interface so that I can look into this? Best, Gregor

Thanks! For me it runs through, although still with the warnings. Could you try to run ```python np.seterr(all="warn") ``` at the beginning of your notebook? I am starting to suspect...

Maybe different column types are the problem? https://github.com/pandas-dev/pandas/issues/17190 Yet that doesn't explain why it works for me, but not for you with the same versions. I'll keep this open and...

Hi @brian-shim, thanks for reporting this. This could be an issue in `upgrade_schema`. To confirm, could you please report the output of ```python t.obs.columns ``` before and after running `upgrade_schema`?...

Ideas of analysis steps that could benefit from Rmarkdown * Now that we have a sample-sheet, could we do an automated DE-analysis using e.g. edgeR or DESeq2? * This is...

afaik it doesn't - it just adds it to `PATH`. Check the `.command.run` script, in there should be a line defining `PATH`.

I'd assume that something goes wrong with mounting the directory in the Docker container.

But would you eventually want to merge this PR, or should we get it in tools first and get it into each pipeline using template sync? Ofc, the tests would...

> The pipeline should be able to handle additional columns already @grst. Cool! I could have sworn there was an issue the last time I tried, but probably I didn't...