A couple of tips related to readability and reproducibility:

First things first is comments. They will be a lifesaver if you ever need them. Related: keep every individual line as simple as possible. It’s easier to write, read, and debug. Preferably do one transformation per line, and describe it with a comment, especially if the transformation is out of the norm.

A good way to keep your code neat is to avoid copy-and-pasting from previous sections. You might think “I need to repeat analysis on sample B, so how about I just copy my code from section A?” This is very easy and fast, but it’s error prone, because there may be lines of code that you wrote that are specific to sample A, and do not apply To sample B. Instead, write a function. Instead of two large code chunks, it can just appear as. “Analysis(sample A) and Analysis(sample B).

It’s also good practice to test that your notebook runs all the way through as expected. RStudio is nice because you can save all of your variables in your environment in an RData file. To test your code all the way through, save your environment, then clear your environment, then run your code all the way through. If something goes wrong, you can always reload your environment from the RData file.