Please cite all software and versions of those software which you use in your methods section, this includes R packages. If you are using R, you can find the citation for your R version with >citation() and for a particular package by using the >citation(“packagename”) function.
Roughly 8% of men, and 1 in 200 women are red-green color blind, so likely will be some of the readers of your paper. Please select a color-blind friendly color scheme for any figures where you use color. http://colorbrewer2.org/ is a great resource for this. If you are using R to make your figures, the RColorBrewer package can be used to easily bring those color schemes into R and apply them to your figures.