I am performing an analysis of targeted proteomics for a study with rather sophisticated study design. As a result of this and other issues (like novelty of the data itself) I found myself writing a lot of custom code (such as visualization, normalization, etc.). The code just begs to organize itself into a package. However, there would be no use for this package except reproducing the data analysis for the corresponding manuscript and/or perhaps exploring the data further. Nonetheless, I really want my data analysis to be reproducible by others and somehow refer to the real code in the manuscript instead of referring to method names (like - this was done by random forest approach [ref]).
So this tentative package doesn't fit the "software" category, because it is not generic enough and tied to a specific study. It doesn't fit into "data" packages because it is not data only. "Annotation" type is out for obvious reasons too. I guess there is always an option to forget about packaging R code all together and provide a long-long script in the supplement.
What would you suggest?