Annotation for Arabidopsis thaliana ?

[benoitballester]

Dear Raymond,

I'd like to use annotatr for Arabidopsis thaliana, but I am not sure if this possible. I have created a regulatory catalogue from an integrative analysis of Arabidopsis thaliana ChIP-seq datasets (http://remap.univ-amu.fr/), and would like to be able to built genome annotation for Arabidopsis thaliana.

Here is what we could use for our human catalogue.

annots <- c("hg38_basicgenes", "hg38_genes_intergenic",
            "hg38_genes_promoters", "hg38_genes_5UTRs", "hg38_genes_3UTRs",
            "hg38_genes_exons", "hg38_genes_introns") 

annotations = build_annotations(genome = "hg38", annotations = annots)

Any advice on how to do that for thaliana ?

Thanks, Ben

[rcavalcante]

Hi Ben,

Thanks for using annotatr. I will look into how easy this is to slot in and let you know. I'm already noticing some divergences in the function assessors with respect to other orgDb packages.

Raymond

[benoitballester]

Thanks Raymond, this would be of great interest for the Plant genomics community

[rcavalcante]

Hi Ben,

I think I can do some refactoring to make it easier for users to use new organisms and other bases for annotations for already supported organisms without much intervention on my part. Your issue is somewhat related to #29, and I think the refactor could solve both at the same time.

As I mentioned in #29, Bioconductor has its next release on Monday (04/27), and with my workload I don't think I can accomplish this by then. However, give me a couple weeks, and I think I'll be able to get this refactored and working.

Thanks for your patience, Raymond

[dktanwar]

Hi,

I would also like to use annotatr for Arabidopsis thaliana. Any update?