Looking at the DESeqDataSetFromTximport() and tximport() functions, I can't find how to set a minimum number of reads per gene, which is necessary for correction of batch effects and recommended for differential expression.

How can I filter genes using tximport?

Thank you.

tximport just imports and builds the matrices. You should do the filtering in whatever downstream package you choose for statistical inference. E.g. with DESeq2, we have examples of how to filter the DESeqDataSet object, once you've created that from the tximport object.