Muhammed Hasan Celik

Your points are right. I think reading vcf files may not be in the scope of the pyranges. But there are interesting use cases. For example, I want to overlap...

Pickling does not help because I need to run the model for different constraints; thus, I need to reinitialize model for multiple time. Moreover for Recon2, when I sample 1e5...

I did not log the constraint; thus, I cannot share it. My Recon version is 2.2. Yes, joblib can convert python object to shared memory. Saying all objects will be...

Hey, I start to work [my fork of cobrapy](https://github.com/muhammedhasan/cobrapy). You may review and give me advice but keep in mind that it is not the final version.

Dear @mnsmar, Can you please share your package version with `pip freeze`?

Hi @MustafaElshani LAPA can create gtf file with novel TES and TSS, when integrated with TALON. Refer to https://github.com/mortazavilab/talon repo first and create GTF from your long-reads. Then you can...

Can you share a section of your bam file with following comment? ``` samtools view -q 10 ${bam_dir}/${bamfile} | head ```

Dear @Priyankanator, It looks like reads in your code not passing some quality filter resulting in 0 counts. Can you further help me to understand what is going on with...

> Hi Please find the results of this command below - [file:///Volumes/salomonis2/LabFiles/Priyanka/LAPA/LAPA_troubleshooting.html](https://github.com/mortazavilab/lapa/issues/url) I cannot access to this url.

Thanks a lot for updating the code for the latest Seaborn! I appreciate your efforts to maintain this repo.