How to retrieve the transcript from gff file with the longest isoform? I tried using R , Biophython and other software also in ubuntu, but got so many installation problems.

If you anyone could help in solving this, it will be helpful.

The R script as follows,

 proteome <- biomartr::getProteome(db = "refseq", organism = "Arabidopsis thaliana")
annotation <- biomartr::getGFF(db = "refseq", organism = "Arabidopsis thaliana")
# retrieve longest isoforms and store in new file
retrieve_longest_isoforms(proteome_file = proteome, 
                          annotation_file = annotation, 
                          new_file = "Athaliana_pep_longest.fa")
# import new file into R session                          
Athaliana_pep_longest <- Biostrings::readAAStringSet("Athaliana_pep_longest.fa")

Thanks in advance. Aneesha

Neither biomartr, nor orthologr are Bioconductor packages, so this isn't the place to ask questions about them.

However, the question you ask and the code you present are different things. You appear to want the 'transcript with the longest isoform,' which could mean lots of different things, really, but the code you present is a way of getting the amino acid sequence for the longest isoform. Those are different things! It is probably pretty trivial to get what you want using Bioconductor, but you need to first define exactly what you are trying to get, and perhaps what you plan to do with it, after which we may be able to provide pointers.