According to the GenomicFeatures annotation and this post it was a conscious decision to not include gene_name in the TxDb objects from the GenomicFeatures package.

Is the decision of not including gene names something that could be brought up again?

I think we can all agree that in the end the majority of end users would like gene names associated with their analysis as these ids are what supply the link to biological knowledge for most people. This - along with the fact that one of the main advantages of Bioconductor is to make data integration easy and seamless - the decision to omit gene names seems a bit out of character?

Apart from this, I also think it is a bit of a shame given the recent push towards us automating away many of the low level data handling hurdles associated with bioinformatics via packages such as tximeta.

Lastly it does seem like the ensembledb package TxDB object contains gene_names so adding them to the regular TxDb would further streamline BioC.

Looking forward to hear your thoughts.

Cheers

Kristoffer

If you want to do mappings that involve a gene ID you can use an OrganismDb package.

> library(Homo.sapiens)
Loading required package: OrganismDbi
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Warning message:
package 'OrganismDbi' was built under R version 4.0.3 
> columns(Homo.sapiens)
 [1] "ACCNUM"       "ALIAS"        "CDSCHROM"     "CDSEND"       "CDSID"       
 [6] "CDSNAME"      "CDSSTART"     "CDSSTRAND"    "DEFINITION"   "ENSEMBL"     
[11] "ENSEMBLPROT"  "ENSEMBLTRANS" "ENTREZID"     "ENZYME"       "EVIDENCE"    
[16] "EVIDENCEALL"  "EXONCHROM"    "EXONEND"      "EXONID"       "EXONNAME"    
[21] "EXONRANK"     "EXONSTART"    "EXONSTRAND"   "GENEID"       "GENENAME"    
[26] "GO"           "GOALL"        "GOID"         "IPI"          "MAP"         
[31] "OMIM"         "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"        
[36] "PMID"         "PROSITE"      "REFSEQ"       "SYMBOL"       "TERM"        
[41] "TXCHROM"      "TXEND"        "TXID"         "TXNAME"       "TXSTART"     
[46] "TXSTRAND"     "TXTYPE"       "UCSCKG"       "UNIGENE"      "UNIPROT"