JBreunig

> idx = which(promoter_ratio > 0.2 & promoter_ratio < 0.8 & log_cov > 3); x.sp = x.sp[idx,] x.sp This seems to mess up the corresponding downstream metadata. e.g. I get...

Same error with pyscenic install. Can't install pyarrow on Python 3.9.

> Same error with pyscenic install. Can't install pyarrow on Python 3.9. This issue is now fixed for me as install proceeded without issue adding the new ctxcore and other...

Same issue here even with a pretty threadbare adata object. ``` pbmc

Thinking this may be due to recent updates to anndata as my postdoc is able to convert his adata objects back and forth without issue but couldn't convert my h5ad...

> I'm having the same issue converting an anndata h5ad that came from version 0.7.8. @JBreunig what version of anndata is your postdoc using? 0.7.6 and 1.8.1

FYI, I just ran into the same thing only when I tried to use multiple cpus (--cpus). It ran fine with the default 1.

Example code: https://github.com/alexdobin/STAR/issues/774#issuecomment-850477636

Just from an end user perspective, I hadn't recognized spliced is put into adata.X and it seems that the other STARsolo users in the original thread didn't either. For my...

I think that we are waiting for this function to be implemented: https://github.com/aertslab/SCENIC/blob/master/man/importGRNBoostResults.Rd Also referred to here: https://htmlpreview.github.io/?https://github.com/aertslab/SCENIC/blob/master/inst/doc/SCENIC_Running.html#option-b-grnboost-python > We are now ready to run GRNBoost. You can find the...