HMMERutils is a project I did as part of my internship at the Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI) during 2021-2022, supervised by Coral del Val.
As part of my bachelor thesis, I used HMMER to find homologous proteins to Fascin (a protein of clinical interest). Although the main idea was to use the Statistical Coupling Analysis method, I spent most of the time obtaining a curated homologous protein dataset. As a result, we devised HMMERutils: An R library for homologous sequences using the HMMER API, taxonomical annotation, calculate physicochemical properties, and facilitate exploratory analysis of homologous sequence data
I haven’t found the time to upload it to BioConductor yet (and at this rate, I never will). Still, it was a super enriching experience to learn the guts of an R package, testing, and contiguous integration with GitHub Actions.
In this regard, the book R Packages by Hadley Wickham and Jennifer Bryan was the resource I used the most (and it is free). I can’t recommend it highly enough.
If you are interested in the library you can of course visit the vignette: HMMERutils in a nutshell.