I was given a table of salmon transcript level quantifications for 75 samples and I am hoping to generate gene level summaries. I can create the database that describes the tx2gene connection (ensembl annotations) but does tximport or another tool have the ability to do the tx to gene level count conversion from the table as opposed to the multiple files that salmon normally outputs?

Thanks, -Lauren

The function summarizeToGene is intended to summarize the counts and abundances to gene level summaries. But it (so far as I can tell) expects the input to be a list containing a matrix of counts, a matrix of abundances, and a vector of transcript lengths. If you don't have that, or cannot easily generate it, you would probably be better off just getting all the salmon output and starting from scratch.