Our lab has been using JMP for clinical data analysis and mouse data analysis, mostly to account for donor variance and batch differences between mouse experiments. JMP is pretty expensive though, so are these things we could do in R? I know stats and plotting can all be done on R in general, but I'm not exactly sure what JMP does to account for donor/batch differences to find a starting point to learn it in R.

Or is there something cheaper or free that would work? I'd like to avoid the 1400 USD/year price tag, partly because they seem so anti-open source while charging absurd amounts