Hi Caibin,

I tried using scar's output as input for TotalVI/SCVI. As expected, those gave an error because the input is not integer anymore. I would suggest implementing stochastic rounding to integers as done in SoupX.

Let me know if you're interested and I can find the time to implement it.

Regards, Mikhael

Hi @fgypas , I made a new release v0.4.1 but bioconda somehow is not triggered upon the new release.

In the new release, some codes related to building process have been refactored.

• All information in setup.py (deleted) is integrated into setup.cfg.
• An extra pyproject.toml file is added.

I am wondering whether these affect the bioconda-recipes.

Many thanks, Caibin

Hi @fgypas ,

I am making a new release. There are mainly three changes: 1) addition of a readthedocs; 2) code reformatting via black and pylint (pylint now can score >7, so I have increase the standard in the Action test from 0.5 to 6); 3) renaming 'scAR' to 'scar'.

I have a couple of questions regarding whether these changes influence the bioconda recipe.

• Will renaming package name (scAR) require modification in bioconda PR? All uppercase ('scAR') is changed to lowercase ('scar') in everywhere possible (inc. folder, environment, and etc.) But the repo name may stay as 'scAR' for a while, as renaming repo name requires permission from Nick.

• Should we exclude the folder of datasets in the conda recipe? In addition, a folder, named 'datasets' contains >100 MBs data is added for the tutorial. Should we exclude it?

Hi scAR team,

I'm reaching out to gauge interest in having a mirror implementation in scvi-tools for scAR. Given the existing infrastructure in the scvi-tools repository, I was able to create a port of scAR quite easily as an external module. Of course, the implementation will link to this repository as the original and cites the paper in the docs. On top of that, the port would allow users of scvi-tools to use the pretrained scAR encoder for doublet detection using the solo model.

Here's the pending pull request so you can check out what it would look like in the final implementation: https://github.com/scverse/scvi-tools/pull/1683

Please let me know what you think!

Hi scar team!

Thank you for developing this interesting package. I had a question about the resulting denoised values for CITE-seq experiments.

I've noticed that some cells that originally have a 0 value for an ADT (as a raw count) will have a positive value (>0) for that ADT after the denoising procedure. Below, I show this case for the CD25 ADT in the 10xPBMC5k CITE-seq dataset (from the tutorial at https://scar-tutorials.readthedocs.io/en/latest/tutorials/scAR_tutorial_denoising_CITEseq.html).

I'm a bit confused about how to best interpret these values and how they are occurring. Should these be set to 0 after the denoising procedure?

Hello,

I was wondering what the recommendations for the sparsity value would be in denoising mRNA? Specifically if we don't know too much of the data besides UMI/nGenes in the cells etc.? I noticed its generally set at 1 for sgRNA decontamination, but what would the general recommended value be for mRNA?

Thanks, Chang

Dear scAR-Team,

thank you for developing this package. I am currently exploring it and I would like to ask you

1. how do you determine the number of epochs the user should use for feature_type = "mRNA"? In your tutorials you used 400 epochs and in your paper you mentioned that you fixed the epochs to 800. I applied it for various batch sizes (up to 1000) and noticed that the model is sensitive to it.

2. I noticed that you use rather small batch-size - is scAR sensitive to the batch-size, it is just due to computational limitations or due to better perfromance?

Thank you in advance!

Best,

fix(*): changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes fix semantic release

Hi @kliatsko ,

We are currently refactoring and adding functionalities to scAR.

Could you please grant the Webhooks permission for us to automate the documentation?

Many thanks in advance. Best regards, Caibin on behalf of the scar team @fgypas @Tobias-Ternent @mr-nvs @AlexMTYZ.

• Additions of readthedocs
• Code refactoring

1. Renaming module names, e.g. changing "scAR" -> "scar"
2. Renaming parameter names, e.g.

changing "scRNAseq_tech" -> "feature_type" changing "model" -> "count_model" changing "scRNAseq_tech" -> "feature_type"

• Black and Pylint re-formatting the code

Addition of black github action that runs on every push and every pull request. It shows in the stdout all the changes that need to be made (--diff), but returns exit code 0, even if errors are observed.