Question: Error when calling AnnotationHub()
0
25 days ago by

Hii,

I am getting use to the Seurat scRNA seq pipeline and as I am trying to obtain gene names for cell cycle genes from Ensembl IDs, I have tried to use Annotation Hub R package to query Ensembl using the ensembldb R package All of the cell cycle genes are Ensembl IDs, but our gene IDs are the gene names. To score the genes in our count matrix for cell cycle, we need to obtain the gene names for the cell cycle genes.

We can use annotation databases to acquire these IDs. While there are many different options, including BioMart, AnnotationDBI, and AnnotationHub. We will use the AnnotationHub R package to query Ensembl using the ensembldb R package.

I get the following error when I try to connect:

> AnnotationHub()
local file path: ‘C:\Users\delriosa\AppData\Local\AnnotationHub\AnnotationHub\Cache/fc476662152_annotationhub.sqlite3’
reason: Failed to connect to annotationhub.bioconductor.org port 443: Connection refused
rid: BFC11


I tried uninstalling and reinstalling, but can´t make it work.

annotation • 57 views
written 25 days ago by albadrs.9310
1

Are you behind a proxy? The proxy will need to be set if so. This can be done by passing as an argument directly in the constructor AnnotationHub(proxy=<value>) or though setAnnotationHubOptions("PROXY", <value>) before running the constructor.

1

That was indeed the problem!

Thanks a lot