R-outbreak-info

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Unable to install library(outbreakinfo)

4

Hi, the comand install.packages("outbreakinfo") doesn't work . The warning message is that the "outbreakinfo" is not available on that version of R. I currently use Rstudio 2022.07.2, R version 4.2.1...

carlottaolivero

Unable to register GISAID credentials

6

Hi! I have a problem authenticating my account. I have a user who works on the Gisaid page. But when I try to authenticate, it doesn't allow me

mecalderon

lookupSublineages("Omicron") right now is missing all the XBB lineages since it's not pulling recombinant lineages.

flaneuse

Info on [contributing packages](https://bioconductor.org/developers/)

flaneuse

I am new to this area and I want to get a lineages frequency plot of a certain location. I found the function can only define 'ndays'. What should I...

B0HA0

more accurate getPrevalence() warning for deletions

1

A response to #81 which raised the issue of the inaccurate and confusing error message in the GetGenomicsData() API: ``` In getGenomicData(query_url = "prevalence-by-location", pangolin_lineage = pangolin_lineage, : Mutations should...

TKMarkCheng

Possible to suppress "Is this a location of interest? (Y/N)" prompts?

5

I'd like to run the outbreak.info `getPrevalence() ` function as part of a high-throughput workflow on an HPC cluster. For context, that part of the workflow is meant to download...

nrminor

I am trying to remove the enabled by GISAID tag under each individual graph in ggarrange. Of course, I would put this tag on my completed, aggregated graph. I attached...

mobrien-15

Genomics API: getPrevalence() does not accept deletions

1

_Submitted by user:_ I noticed a pretty significant limitation in the getPrevalence() function: the function does not accept deletions. This is the error message I’ve seen (using a deletion found...

EmilyHaag

Could the authenticate user function be updated to accept a username and password

2

Hi - would it be possible to update the authenticateuser() function so that it accepts a username and password and passes those automatically to the GISAID site (I think this...

amishcode