I have performed an analysis of the differential expression of genes in an experiment and have acquired the results which state which genes are significantly differentially expressed relative to my control. But I was wondering if there was a script in which to sort these significantly differentially expressed transcripts together based on functional group (i.e., nitrate metabolism, carbon fixation). Any help would be greatly appreciated!

This has little to do with DESeq2, per se. Your next step should be to perform some type of gene enrichment. Programs that I use routinely for this purpose include:

• topGO (Bioc)
• KEGGprofile (Bioc)
• enrichR (CRAN)

There are many other gene enrichment programs out there; so, take some time to search about. Note that enrichR links up to many databases / repositories, i.e., it aggregates enrichment results from multiple sources.

Kevin