Kseniya Petrova

It seems that all the single-cell technologies should be strand-specific because of the library preparation process, it's strange not to use that fact in gene counting. Or I'm not right

> In the help documentation of sc.pp.scale, it is said "zero_center If `False`, omit zero-centering variables, which allows to handle sparse input efficiently. I am still confused about zero_center. If...

As far as I understand, it checks the flag IsPrimaryAlignment, usually secondary alignments are marked with a secondary alignment flag.

The other issue that I've encountered that the code doesn't work if `FindMarkers` [here in SignacBoot](https://github.com/mathewchamberlain/SignacX/blob/master/R/helper_functions.R#L279) returns 0 or 1 marker genes with `avg_log2FC < 0`. So I wonder if...

Hi @Sirin24 ! 1. No, you don't have to run harmony on the reference dataset if it's been already batch-corrected, just follow the instructions for [Symphonypy without harmony tutorial](https://symphonypy.readthedocs.io/en/latest/Symphonypy_without_harmony_tutorial.html). It...

Hi @Flu09! I'm so sorry that you are encountering this bug! What's the datatype of your sparse matrix adata_query.X in the example above?

Eh, float64 seems to be OK, I was just hoping that it's connected this bug with np.float16: https://stackoverflow.com/questions/40046118/why-cant-i-assign-data-to-part-of-sparse-matrix-in-the-first-try

@Flu09 Don't you mind sharing the least subsample of data to reproduce the error? Probably it could be a couple of cells per dataset.

Probably related to https://github.com/scverse/anndata/issues/1349?

@Flu09 I'm so sorry, could you please share a small subset of your data :(