I was looking to some examples and I could retrieve the microRNAs of the hg19 transcriptome, but not from the hg38 transcript annotation.

I realized this might be because TxDb.Hsapiens.UCSC.hg38.knownGene doesn't have a miRBase build ID, which I expected to be GRCh38. I see that supportedMiRBaseBuildValues() have the mirbase.db for Homo sapiens with the GRCh37.p5, which I don't know if it is related or not.

Is there a way to retrieve microRNAs annotation for the hg38 (other than microRNAs())?

See code below:

suppressPackageStartupMessages(library("TxDb.Hsapiens.UCSC.hg19.knownGene"))
TxDb.Hsapiens.UCSC.hg19.knownGene
#> TxDb object:
#> # Db type: TxDb
#> # Supporting package: GenomicFeatures
#> # Data source: UCSC
#> # Genome: hg19
#> # Organism: Homo sapiens
#> # Taxonomy ID: 9606
#> # UCSC Table: knownGene
#> # Resource URL: http://genome.ucsc.edu/
#> # Type of Gene ID: Entrez Gene ID
#> # Full dataset: yes
#> # miRBase build ID: GRCh37
#> # transcript_nrow: 82960
#> # exon_nrow: 289969
#> # cds_nrow: 237533
#> # Db created by: GenomicFeatures package from Bioconductor
#> # Creation time: 2015-10-07 18:11:28 +0000 (Wed, 07 Oct 2015)
#> # GenomicFeatures version at creation time: 1.21.30
#> # RSQLite version at creation time: 1.0.0
#> # DBSCHEMAVERSION: 1.1
suppressPackageStartupMessages(library("TxDb.Hsapiens.UCSC.hg38.knownGene"))
microRNAs(TxDb.Hsapiens.UCSC.hg38.knownGene)
#> Error in microRNAs(TxDb.Hsapiens.UCSC.hg38.knownGene) : 
#>  this TxDb does not have a miRBase build ID specified
TxDb.Hsapiens.UCSC.hg38.knownGene
#> TxDb object:
#> # Db type: TxDb
#> # Supporting package: GenomicFeatures
#> # Data source: UCSC
#> # Genome: hg38
#> # Organism: Homo sapiens
#> # Taxonomy ID: 9606
#> # UCSC Table: knownGene
#> # UCSC Track: GENCODE V41
#> # Resource URL: http://genome.ucsc.edu/
#> # Type of Gene ID: Entrez Gene ID
#> # Full dataset: yes
#> # miRBase build ID: NA
#> # Nb of transcripts: 272352
#> # Db created by: GenomicFeatures package from Bioconductor
#> # Creation time: 2022-09-27 15:30:34 +0000 (Tue, 27 Sep 2022)
#> # GenomicFeatures version at creation time: 1.49.6
#> # RSQLite version at creation time: 2.2.17
#> # DBSCHEMAVERSION: 1.2

Created on 2023-01-09 with reprex v2.0.2

Hypothetically can just make your own TxDb package, and include the correct genome build in the call to makeTxDbPackageFromUCSC. Unfortunately, the microRNAs function uses the mirbase.db package, which doesn't contain any GRCh38 data, so it's probably a moot point, unless you can get James Reid to either update mirbase.db to include GRCh38 data (contingent upon such data existing), or you could maybe roll your own functions.