Nadav Brandes

Hi, You need to first convert the sequences to the .lf format. It is a very simple FASTA-like format. You can see examples here: https://github.com/ddofer/asap/tree/master/data/phosphoserine Also, I recommend you to...

There is no automatic tool that does this conversion; you will have to write some code to do that. Fortunately, the format is super simple. On Thu, Aug 9, 2018...

You can do whatever you want with the code. We just ask that if you find our work useful, please cite our paper (ASAP: a machine learning framework for local...

We were also wondering the same thing. We are trying to use freemuxlet to call the genotypes of single cells. We were wondering about the ALLELES column in the .plp.gz...

@Basso42 I purchased more LFS quota. Does it work now?

@Basso42 Once you resolve the dependencies, if you're willing to upload the dependencies file to GitHub, that would be appreciated (you can make a pull request).

@dp9090 Your question doesn't seem related to this issue. I also think it's been asked and answered in the past. Please run a quick search over our past Issues. If...

Are you running the most updated version of ProteinBERT (from GitHub) with the recommended package versions? Did you manage to download the pickle file with the pretrained model? Maybe try...

I think it can be run without covariates, but it is really not recommended. Without at least including the ~5 first PCs of genetic variation, you are likely to get...

40GB should be more than enough to run ProteinBERT (we trained it on a 16GB GPU). The amount of GPU memory used should only depend on the batch size (and...