I have RNASeq counts for one gene that was treated with 12 different drugs (with 3 replicates each). I was wondering if anyone could please tell me which R package I should use to detect differential gene expression to identify which treatment has the greatest effect on expression of this gene?

Thanks :) ```

It is impossible to do an analysis of RNA-seq counts if you only have data for one gene. You need counts for all genes in order to undertake an analysis, or at very least you would need to know the total library size for each replicate.

If you have complete RNA-seq data, then you just conduct a standard RNA-seq analysis for all genes and then select the gene you're interested in. The tags added to your question show that you already know Bioconductor packages suitable for that task.