R resources and programming

Introduction to R pdf notes on R: A Programming Environment for Data Analysis and Graphics. The official CRAN intro by Venables et al..
Advanced R Companion website by H. Wickham.
Writing R packages Useful information on the topic by H. Wickham. And more on the topic:
Writing R extensions
Making simple packages
Making packages under Windows
esoteric R Doing things well in R, compiled by J. Ryan.
Using C code in R Short pdf guide to the .C interface by R. Peng & J. de Leeuw.
R cheat sheets on various topics, by RStudio.
R CRAN packages overview by name for thousands of R packages on the CRAN repository.
R bioconductor packages overview by name for thousands of R packages listed by bioconductor.
Software licences explained.

Featured packages and websites

Shiny tutorial #1 on how to use R outputs interactively in a web browser, by RStudio.
Shiny tutorial #2 by P. Hiemstra.
devtools makes package development easier.
Interactive isotope pattern calculation based on the R enviPat package.
Interactive homologue series detection based on the R nontarget package.
Proteowizard for MS file conversion and centroidization.
ms-utils.org lists plenty of open-source software tools for mass spectrometric analysis.