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Bioconductor / AnnotationHub

Client for the Bioconductor AnnotationHub web resource
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Human EnsemblDB v112 is only available for GRCh37 #53

Closed zyh4482 closed 3 weeks ago

zyh4482 commented 3 weeks ago

Hello there.

Could you please check if ensembl database of GRCh38 for human species is available? I could only reach the GRCh37 genome build. 

> AnnotationHub::query(ah, pattern = c("EnsDb","Homo sapiens","GRCh38"))
AnnotationHub with 26 records
# snapshotDate(): 2024-04-30
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
#   tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53211"]]' 

             title                             
  AH53211  | Ensembl 87 EnsDb for Homo Sapiens 
  AH53715  | Ensembl 88 EnsDb for Homo Sapiens 
  AH56681  | Ensembl 89 EnsDb for Homo Sapiens 
  AH57757  | Ensembl 90 EnsDb for Homo Sapiens 
  AH60773  | Ensembl 91 EnsDb for Homo Sapiens 
  ...        ...                               
  AH104864 | Ensembl 107 EnsDb for Homo sapiens
  AH109336 | Ensembl 108 EnsDb for Homo sapiens
  AH109606 | Ensembl 109 EnsDb for Homo sapiens
  AH113665 | Ensembl 110 EnsDb for Homo sapiens
  AH116291 | Ensembl 111 EnsDb for Homo sapiens
> AnnotationHub::query(ah, pattern = c("EnsDb","Homo sapiens"))
AnnotationHub with 27 records
# snapshotDate(): 2024-04-30
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
#   tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53211"]]' 

             title                             
  AH53211  | Ensembl 87 EnsDb for Homo Sapiens 
  AH53715  | Ensembl 88 EnsDb for Homo Sapiens 
  AH56681  | Ensembl 89 EnsDb for Homo Sapiens 
  AH57757  | Ensembl 90 EnsDb for Homo Sapiens 
  AH60773  | Ensembl 91 EnsDb for Homo Sapiens 
  ...        ...                               
  AH109336 | Ensembl 108 EnsDb for Homo sapiens
  AH109606 | Ensembl 109 EnsDb for Homo sapiens
  AH113665 | Ensembl 110 EnsDb for Homo sapiens
  AH116291 | Ensembl 111 EnsDb for Homo sapiens
  AH116860 | Ensembl 112 EnsDb for Homo sapiens

See also in this issue

lshep commented 3 weeks ago

The maintainer of these resources is the repository you have linked too here. Per that issue they have identified the problem and are regenerating objects to be loaded; when they provide new resources it will become available.