At which part of the paper is it better to cite R packages? I'm sure we need to pay credit to every R package developer. Just in line with this post.  

My question is, how better to integrate the citations of R packages into my paper. Should it be part of the methodological part? I saw papers that just throw the citations into the reference list. But it just doest not seem right.



There is a similar question on Academia. My focus is on the way one should incorporate the actual citations into the paper.
You should cite the software packages that you use just like any other piece of scientific work that you build on. If they are significant enough to make it to your main narrative, then cite them there just like the other key techniques you build upon. If they are useful but uninteresting methodological detail (e.g., equivalent to a microscope model or reagent brand) then they should  in just the same way be relegated to an equivalent methods section, appendix, or other piece of supplemental material.