If I run the following code to get RefSeq from UCSC:
library(AnnotationHub) ahub <- AnnotationHub() ahub <- subset(ahub, species == "Homo sapiens" & genome == "hg19") query(ahub, "refseq")
> query(ahub, "refseq") AnnotationHub with 1 record # snapshotDate(): 2018-08-01 # names(): AH5040 # $dataprovider: UCSC # $species: Homo sapiens # $rdataclass: GRanges # $rdatadateadded: 2013-03-26 # $title: RefSeq Genes <SNIP>
suggesting to me that this data is from 2013. Additionally, if I change
hg38 my query comes up empty, despite the fact that UCSC at least right now has RefSeq genes released in 2018 for hg38 (as everyone would expect).
Question: I am surprised that AnnotationHub has these (to me) outdated resources. I expected that that with each new Bioc release, the hub gets updated. But perhaps I am wrong?