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This issue will be updated monthly to list new publications from the team ([relevant GitHub Actions job](https://github.com/epiforecasts/epiforecasts.github.io/blob/536d602b8b8bb3c1b2a724bfbe91cceeaf3…
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I would like to addModuleScore to my R object.
If I use my default assay of integrated, then I get errors that my features are not present in my object
If I switch to RNA assay as my default, I ge…
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### Context
Strain names for pathogens can be messy depending on the pathogen and data source.
We would like to provide a way to format strain names using general pattern matching.
See #860 for…
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### Data Type Requested
User Surveys
### Data Source Type
Medallia
### Date Range Start
07-01-2024
### Date Range End
07-31-2024
### Product Name(s)
Sitewide Content, Accessibility, and Infor…
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Hi,
I'm trying to download protein sequences of all Vertebrates using this command. Its running on Redhat 8.3.
`./datasets download genome taxon Vertebrates --exclude-rna --exclude-seq --exclude…
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## Background
After research and readout, it has been decided that Covid status will be removed. We will want to
- modify the editor UI to remove current Covid status option
- work with Content…
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### Checkbox
- [X] I agree to follow [code of conduct](https://lisphilar.github.io/covid19-sir/CODE_OF_CONDUCT.html) and to engage in discussion actively.
- [X] I used [the latest version of covsi…
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## Description
It was observed around 9/20/22 that some CMS-driven pages are missing from `sitemap.xml`. The initial anecdotes were about R&S pages, which were not performing as expected in site se…
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## Context
Prior to the SARS-CoV-2 pandemic, we assumed that Nextstrain workflows would begin with pre-curated sequences and metadata sourced either from our internal database ("fauna") or custom s…
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I’m somehow not getting sequences released on 2024-01-28 when downloading via:
```
datasets download virus genome taxon 10244 --filename data/ncbi_dataset.zip
```
despite them showing on NCBI …