Sten Linnarsson

Literally the next line after the one you quoted reads: ``` Note: pysam is also a requirement but currently it is preferable to install it through PyPI wheel (i.e. by...

Aha, ok I get it. That seems wrong, because pysam includes htslib (which is samtools), as far as I understand. Or maybe I'm misunderstanding, and you're saying that samtools can...

Ok, I never noticed probably because I had samtools installed for some other reason. If the code is not too complicated and you want to drop the dependency on samtools...

I think actually the error is related to the second and third exceptions rather than the first (which is handled properly by velocyto). These two errors: ``` ValueError: All chunk...

I think the issue is that py-backwards converts ```python f"Hello {key: >10} {x: >5} world" ``` into ```python ''.join(['Hello ', '{: >10}'.format(key), ' ', '{: >5}'.format(x), ' world']) ``` So,...

Oh, I realize you need to put the actual expressions in the arguments (since f-strings allow expressions inside the curly braces). So it would have to be something like: ```python...

There are many ways to create a loom file (see [loompy.org](http://loompy.org), especially the documentation), including from an expression matrix (e.g. from a 10x cellranger output). However, in order to run...

To save tSNE and cluster name attributes into the loom file, do this; ```python import loompy with loompy.connect("mydata.loom") as ds: ds.ca.TSNE1 = ... # a list or numpy array of...

To clarify, none of the Euclidean distances should actually be infinite, so this is a bug caused somehow by a specific random seed. The input data range `X.min(), X.max()` is...

Thanks, & thanks for developing pynndescent and UMAP! They are true workhorses for the single-cell analysis community. Btw - for anyone else who hits this issue - the workaround was...