Is there a package version of EnsDb.Rnorvegicus that is based on the newer version of Rattus Norvegicus reference Rnor6? All I could find is v79 which is based on older reference Rnor5. Thanks Kerem

Yes, please have a look at the excellent ENSEMBL-based annotation packages Johannes Rainer provides through the AnnotationHub!

See below for some code to get you started. Note that I am using ENSEMBL v100, but if needed you can easily create a EnsDb for another ENSEMBL version!

> # if needed, install required libraries.
> BiocManager::install(c("AnnotationHub", "ensembldb", "AnnotationForge")
> 
> library(AnnotationHub)
> library(ensembldb)
> library(AnnotationForge)
>
> # start an AnnotationHub instance/connection.
> ah <- AnnotationHub()
snapshotDate(): 2020-04-27
> 
> # query for availabel Rat Ensembl databases
> EnsDb.rat <- query(ah, c("EnsDb", "Rattus norvegicus"))
> EnsDb.rat
AnnotationHub with 14 records
# snapshotDate(): 2020-04-27
# $dataprovider: Ensembl
# $species: Rattus norvegicus
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53239"]]' 

            title                                  
  AH53239 | Ensembl 87 EnsDb for Rattus Norvegicus 
  AH53743 | Ensembl 88 EnsDb for Rattus Norvegicus 
  AH56709 | Ensembl 89 EnsDb for Rattus Norvegicus 
  AH57792 | Ensembl 90 EnsDb for Rattus Norvegicus 
  AH60814 | Ensembl 91 EnsDb for Rattus Norvegicus 
  ...       ...                                    
  AH69261 | Ensembl 96 EnsDb for Rattus norvegicus 
  AH73956 | Ensembl 97 EnsDb for Rattus norvegicus 
  AH75088 | Ensembl 98 EnsDb for Rattus norvegicus 
  AH78871 | Ensembl 99 EnsDb for Rattus norvegicus 
  AH79776 | Ensembl 100 EnsDb for Rattus norvegicus
>
> # Fetch the v100 EnsDb and put it in the cache.
> EnsDb.rat <- EnsDb.rat[["AH79776"]]
>
> #check
> columns(EnsDb.rat)
 [1] "DESCRIPTION"         "ENTREZID"            "EXONID"             
 [4] "EXONIDX"             "EXONSEQEND"          "EXONSEQSTART"       
 [7] "GCCONTENT"           "GENEBIOTYPE"         "GENEID"             
   <<snip>>
> 
> 
> # Now copy, and install the database locally.
> # By doing so, you can just quickly load the library next time.
> # see: ?makeEnsembldbPackage
> 
> #set working dir to store the relaively large files.
> setwd("E:\\myDir")
>
> #copy databse from the cache to working dir
> file.copy(AnnotationHub::cache(ah["AH79776"]), "./EnsDb.rat.sqlite")
 [1] TRUE
>
> # now make it a package. Change name and email accordingly
> makeEnsembldbPackage("EnsDb.rat.sqlite", version="0.0.1",
+     maintainer = "First Name <first.last@mydomain.com>",
+     author = "First Name <first.last@mydomain.com>",
+     destDir=".", license="Artistic-2.0")
Creating package in ./EnsDb.Rnorvegicus.v100 
[1] TRUE
>
>
> # install package in R.  
> # note modifed name of created directory (not EnsDb.rat... but EnsDb.Rnorvegicus.v100)
> install.packages("./EnsDb.Rnorvegicus.v100", type = "source", repos = NULL)
* installing *source* package 'EnsDb.Rnorvegicus.v100' ...
** using staged installation
* DONE (EnsDb.Rnorvegicus.v100)
> 
> #check: 
> library(EnsDb.Rnorvegicus.v100)
> EnsDb.Rnorvegicus.v100
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.3.5
|Creation time: Sat May  2 05:29:36 2020
|ensembl_version: 100
|ensembl_host: localhost
|Organism: Rattus norvegicus
|taxonomy_id: 10116
|genome_build: Rnor_6.0
|DBSCHEMAVERSION: 2.1
| No. of genes: 32883.
| No. of transcripts: 41078.
|Protein data available.
>
> columns(EnsDb.Rnorvegicus.v100)
 [1] "DESCRIPTION"         "ENTREZID"            "EXONID"             
  <<snip>>      
[37] "UNIPROTID"           "UNIPROTMAPPINGTYPE" 
>