Michaela Müller

Hi, unfortunately DROP doesn't include the external samples when checking, but we're working on it. We set 10 samples as the minimum, but would recommend at least 30 samples for...

Hi, is this PR still being worked on?

Is PATH your project directory or is it a subdirectory? If so, could you add the following above line 14? ``` print(wbuild.utils.Config()) print(projectDir) ``` Also, make sure that you're running...

So instead of using the sample annotation file as input, it would be better to evaluate the necessary sample runs via config and then feed that into the final target

Sorry for the late reply. 1. The tmp folder is ID specific, so I would assume it is run specific, as Snakemake shouldn't be running two IDs twice. 2. I...

Tests are failing, I believe, because the gene_list genes are removed from control genes before random sampling, not after, resulting in a different control gene set. Not quite sure why...

To answer the following question: > 2. what you said: The original approach samples from the full list of genes in each bin, then restricts the sample to valid ones....

About question 1: I find also it strange that the order of cuts that you iterate though should have such a large effect on sampling. Should I change it back...

This error happened to me too when working on a small dataset and scoring a single gene with ctrl_size=1. This happens at random in the following line: https://github.com/scverse/scanpy/blob/383a61b2db0c45ba622f231f01d0e7546d99566b/scanpy/tools/_score_genes.py#L168 I was...

I’d consider the issue to be a bug, can we label it as such?