Hi,

I wonder if there is a sheep-specific genome database package for sheep, such as EnsDb.Hsapiens.v86 in human. I could only find a package for Affymetrix data in sheep.

Thank you, Priscila

Yes, there is!

An EnsDb for sheep can be obtained through the so-called AnnotationHub.

See James' and my posts in the thread linked to for all code. Note that these were used to obtain a EnsDb for rat, but the code is easily changed.

EnsDb.Rnorvegicus for Rnor6

The key difference is thus to query for sheep (and not rat):

> library(AnnotationHub)
> library(ensembldb)
> library(AnnotationForge)
> 
> ## start an AnnotationHub instance/connection.
> ah <- AnnotationHub()
snapshotDate(): 2022-10-31
> 
> ## query for available Sheep EnsDb
> EnsDb.sheep <- query(ah, c("EnsDb", "Ovis aries"))
> EnsDb.sheep
AnnotationHub with 21 records
# snapshotDate(): 2022-10-31
# $dataprovider: Ensembl
# $species: Ovis aries
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53225"]]' 

             title                           
  AH53225  | Ensembl 87 EnsDb for Ovis Aries 
  AH53729  | Ensembl 88 EnsDb for Ovis Aries 
  AH56695  | Ensembl 89 EnsDb for Ovis Aries 
  AH57777  | Ensembl 90 EnsDb for Ovis Aries 
  AH60796  | Ensembl 91 EnsDb for Ovis Aries 
  ...        ...                             
  AH95797  | Ensembl 104 EnsDb for Ovis aries
  AH98100  | Ensembl 105 EnsDb for Ovis aries
  AH100696 | Ensembl 106 EnsDb for Ovis aries
  AH104917 | Ensembl 107 EnsDb for Ovis aries
  AH109389 | Ensembl 108 EnsDb for Ovis aries
> 
>
> ## Fetch the v108 EnsDb and put it in the cache.
> EnsDb.sheep <- EnsDb.sheep[["AH109389"]]
downloading 1 resources
retrieving 1 resource
loading from cache
> 
> ##check
> columns(EnsDb.sheep)
 [1] "CANONICALTRANSCRIPT" "DESCRIPTION"         "ENTREZID"           
 [4] "EXONID"              "EXONIDX"             "EXONSEQEND"         
 [7] "EXONSEQSTART"        "GCCONTENT"           "GENEBIOTYPE"        
[10] "GENEID"              "GENEIDVERSION"       "GENENAME"           
[13] "GENESEQEND"          "GENESEQSTART"        "INTERPROACCESSION"  
[16] "ISCIRCULAR"          "PROTDOMEND"          "PROTDOMSTART"       
[19] "PROTEINDOMAINID"     "PROTEINDOMAINSOURCE" "PROTEINID"          
[22] "PROTEINSEQUENCE"     "SEQCOORDSYSTEM"      "SEQLENGTH"          
[25] "SEQNAME"             "SEQSTRAND"           "SYMBOL"             
[28] "TXBIOTYPE"           "TXCDSSEQEND"         "TXCDSSEQSTART"      
[31] "TXEXTERNALNAME"      "TXID"                "TXIDVERSION"        
[34] "TXISCANONICAL"       "TXNAME"              "TXSEQEND"           
[37] "TXSEQSTART"          "TXSUPPORTLEVEL"      "UNIPROTDB"          
[40] "UNIPROTID"           "UNIPROTMAPPINGTYPE" 
>
> ## and so on...