I am regularly using the annotationHub to retrieve/query the Ensembl-based gene annotations (ensembldb). This works fine for e.g human and mouse, but I now would like to obtain info made available through the Ensembl Plant database; specifically for Arabidopsis ( http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index ).
Question: Is such ensembldb available at the annotationHub? I searched for it but could not find it...
while it is possible to create EnsDb databases also for ensemblgenomes (including plants, funghi etc) I did not do this on a regular basis and was also hesitant to add these to AnnotationHub because I was not sure how many users there will be for these.
Just let me know which species (for which Ensembl/Ensemblgenomes) version you need and I will create the EnsDb for you.
First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant community ^^
I have been trying to find a good Arabidopsis thaliana annotation for single cell ATAC seq analysis, and downloaded the Arabidopsis Annotation you created 4.5 years ago. But Unfortunately R display the error "Annotation must be a GRanges object"
Despite trying to convert it using different program but did not succeed.
Would you have a solution about that ?