maxim-h

Outdated scanpy dependency

1

Thank you for your cool package. I've been experimenting with it on my own data lately. The issue that arose after installing it (from PyPI) is that the 'scanpy==1.4.6' dependency...

This is meant to help diagnose issues when assay doesn't have desired layer. For example see satijalab/seurat#8658 and discussion in satijalab/seurat#8659, specifically the [suggestion from Sam](https://github.com/satijalab/seurat/pull/8659#issuecomment-2009820323). The warning message might...

Image links to /articles are broken.

1

Hey, thanks for all the great work! I saw somewhat similar issues, but not exactly this, so I thought maybe it's not reported yet. Seems like all the blog posts...

Local paths in requirements.txt

3

I've noticed that `requirements.txt` mostly consists of `@ file` references, so it's not really usable. Would be nice to have it since I don't use conda for this.

While trying the vanilla analysis from the vignette after the following call: ```r run_atac("ChrAccR_analysis", "bamFilenameFull", sampleAnnot, genome="hg38", sampleIdCol="sampleId", regionSets=regionSetList) ``` I get the error: ``` Error: 'getRealizationBackend' is defunct. Use...