Differentially gene expression analysis with RNA-seq data is quite common nowadays, and there are pretty good Bioconductor packages for that: limma::voom, DESeq2 …
The code for that part is quite simple, being super quick to get a list of de-regulated genes. However, downstream analyses vary a lot depending on the project itself. But I found myself doing the same plots and analyses many times for different project, so I put together a bunch of plots and analyses using code from my colleagues at work (@HSPH bioinformatics core) and myself.