Zhi-Jie Cao

Well, that's weird... I have never seen anything like that. Maybe it's something in this data that triggered a bug in the model. Would you mind if you share the...

Thanks for your interest in Cell BLAST! The current version (v0.3.8) depends on the old TensorFlow v1. We will be changing the backend to PyTorch in the coming release ([v0.5.0](https://github.com/gao-lab/Cell_BLAST/releases/tag/v0.5.0)),...

Sorry for the late response. I tried but could not reproduce this error with subsampled cells. In this particular example, it looks like the direct cause is a lack of...

Thanks for your interest in GLUE! Yes you can use the cell embeddings for clustering. E.g., in `scanpy` the following should do: ```py combined = ad.concat([rna, atac]) sc.pp.neighbors(combined, use_rep="X_glue") sc.tl.leiden(combined)...

Hi @CHANG-Shaole. Thanks for your interest in Cell BLAST! To perform cross-species cell type annotation with Cell BLAST, you would need to align the gene names across species using ortholog...

I tried downloading them, and they seem to be working just fine. Could you try a different browser, or use command line tools like `wget` or `curl`?

Hi @Khalid-Usman! Which lines did you comment out in the config file? There are multiple types of benchmarks in the config file, you may try commenting out all but one...

Oh that should be a problem with the snakemake profile. Unless you are using a `slurm` cluster, the `local` profile should be used: ```sh snakemake -j32 --profile profiles/local # On...

Sorry for the late reply! Could you check the log files for more detailed errors? E.g., "s01_preprocessing_nbconvert.log"?

Hi @Khalid-Usman! In that case you may need to modify the [kernel spec section in e01_inmf.R](https://github.com/gao-lab/GLUE/blob/fc6c2093ecc218e686586eb5fd4ea5f3e7a87e13/experiments/TripleOmics/e01_inmf.R#L10) to match your installed IRkernel version, likely: ``` # kernelspec: # display_name: R 4.3.2...