I'm using ArchR to analyze a H.sapiens PBMC scATAC dataset I have and decided to use Ensembl's GRCh38, Release 103 genome as my reference.
In order to do this I needed to use ArchR's
createGeneAnnotation and to define the genome. For
OrgDb object was need which I used AnnotationHub to access.
Once I loaded in this OrgDb I realized there were GENEIDs (EntrezIDs) present in my GTF for GRCh38, Release 103 that were missing from the OrgDb. I thought this meant it wasn't up to date, but realized only one was returned when I queried annotation hub for it like this
query(hub, c("Homo sapiens","OrgDb")).
Is there somewhere I can get a more up to date version of the H.sapiens OrgDb? I was under the impression it was regularly updated so had trouble believing that it was missing so many IDs
Its resulting in detected marker genes being labeled as
Any and all guidance would be greatly appreciated