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Very good job!
As you probably know is now possibile to scrape data directly from the new ISS Dashboard
https://www.epicentro.iss.it/coronavirus/sars-cov-2-dashboard
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Title: SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor
# General Information
## Please paste a link to the paper or a citation here:
…
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A living google doc describing the form and function of different helicases, including the SARS-CoV-2 helicase, Nsp13.
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There seems to be a large KP.3.1.1+S:S31F branch, while KP.3.1.1 shall have S:31del.
That branch is driven by Denmark seqs which do not handle S:S31del well. When Querying C12616T, A13121T, C2165…
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This model is ready for testing. If you are assigned to this issue, please try it out using the CLI, Google Colab and DockerHub and let us know if it works!
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```
downloader = Downloader(data_directory='.')
downloader.add_data_product(namespace='SCRC', data_product='records/SARS-CoV-2/scotland/cases-and-management/carehomes')
downloader.download()
```
…
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## Understanding ir.datasets.vdjdb() and Scirpy's Data Needs
- [x] Go through scirpy documentation
- [x] Go through Jupyter Notebook from Francesca
- [x] Have a look at GitHub issues:
Hackathon idea …
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Title: Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa.
# General Information
L…
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I tried variant calling using bcftools using recommended settings for SARS-Cov-2 i.e. using `--ignore-overlaps --min-ireads 10` on my `ISeq Illumina` data. However, I can see that a deletion supported…
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Dear,
We are looking into how freyja performs plotting on specific lineage (--lineages) on the visualization. We have plot our samples and the visualization display majorities of the lineages were…