My personal favorite resource is "R for Data Science" by Hadley Wickham. It covers lots of nice data manipulation and visualization examples, and provides a good introduction to the tidyverse, which is a particular dialect of R that's well-suited for data analysis. It's available for free at:

https://r4ds.hadley.nz/

For more specialized analytical methods there are lots of textbooks out there that provide a deep dive into packages for a specific field (e.g. survival analysis, machine learning, time series), but for general data manipulation and visualization it's hard to beat R4DS.

[1] will give you a more programming language-focused perspective, as opposed to many other R books.

--

[1] https://adv-r.hadley.nz/

An option to the Hadley book that also covers some nice statistical methods is Statistical Rethinking by McElreath. Not really available for free though but interesting read.