(1) Is TxDb.Athaliana.BioMart.plantsmart51 the TAIR10 gene annotation?
(2) If so, I am unable to install it under R. I ran the code below:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TxDb.Athaliana.BioMart.plantsmart51")
I got the following error:
Warning message:
package ‘TxDb.Athaliana.BioMart.plantsmart51’ is not available for Bioconductor version '3.13'
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Can anyone help me figure out what I did wrong? Thanks very much!
(1) This TxDb annotation for Arabidopsis on BioMart comes from the ENSEMBL Plants release (v)51 and is for the TAIR10 genome sequence.
(2) I believe the TxDb package needs to be updated for your Bioconductor version. However, I can see that there is now a more recent ENSEMBL (and hence BioMart too) release (v54). It would be more beneficial to download the most recent genome annotation either from BioMart, or from ENSEMBL Plants v54, or again directly from TAIR (Arabidopsis.org), and transform it into a TxDb (see their manual).
Note that depending on your application, you might want to stick to the TAIR annotation for precise transcripts start sites and 5'UTRs, or chose the Araport annotation which has more annotated genomic features but lower precision.
Warning message:
package ‘TxDb.Athaliana.BioMart.plantsmart51’ is not available for Bioconductor version '3.13'
You're using an old and unspported version of Bioconductor. TxDb.Athaliana.BioMart.plantsmart51 is available in the current version of Bioconductor, version 3.15. I highly recommend that you update your installation to this version. Note that BioC 3.15 requires the latest R (4.2.1).
