<p>I have been asked to recommend introductory books and resources to R and Bioconductor. My problem is just, I never read a book to learn R or Bioconductor, so I have no experience with this and cannot recommend one. I am interested in mainly introductory books, possibly targeting various groups of readers (computer scientists, molecular biologists, (bio-)statisticians), any recommendation appreciated.  </p>

<p>For example, I used the following resources:</p>

<ul>
<li>The <a href='http://cran.r-project.org/manuals.html'>R-manuals</a>, especially <a href='http://cran.r-project.org/doc/manuals/R-intro.html'>the R intro</a></li>
<li>There are also <a href='http://cran.r-project.org/other-docs.html'>a lot of contributed documents there</a> on the R web site, but I didn't 
use.</li>
<li>If a package from Bioconductor interests me, I read the package vignette.</li>
<li>I read the Bioconductor mailing list, that helps to see what other people use.</li>
<li>I have the "<a href='http://www.springer.com/statistics/computanional+statistics/book/978-0-387-98966-2'>Venebles, Ripley. S Programming</a>" book, that is hardly introductory. </li>
</ul>

<p>Which books did you find helpful or completely useless to learn R/Bioconductor? For example: <a href='http://www.bioconductor.org/pub/RBioinf/'>R Programming for Bioinformatics</a> looks promising, anybody read it?</p>

<p>Or do you share my reluctance towards R-books and prefer online resources?</p>

<p>Theresa Scott's Intro deserves a mention although it can be a bit verbose.</p>

<p><a href="http://biostat.mc.vanderbilt.edu/wiki/pub/Main/TheresaScott/Scott.IntroToR.I.pdf">Introduction to the
Fundamentals &amp; Functionality of
the R Programming Language</a></p>

<p>For Bioconductor and short read analysis I would stick with Girke's cookbook which I have found amazingly helpful. I would gladly have paid $100 for access to it.</p>

<p><a href="http://manuals.bioinformatics.ucr.edu/home/ht-seq"</a> Sequence Analysis with R and Bioconductor
</a></p>

<p>Have not read <a href='http://oreilly.com/catalog/9780596801717'>R in a Nutshell</a> yet but from what I saw in Joseph Adler's <a href='http://oreilly.com/catalog/9780596009427'>Baseball Hacks</a> and the initial reviews I have a good feeling about it.</p>

<p>I would avoid R Programming for Bioinformatics as that book is really geared toward package development.</p>

<p>I co-wrote an O'Reilly Short Cut, "Data Mashups in R", that is designed to be a little more fun than some of the scientific stuff out there while still exploring data manipulation in R, using packages, XML, web services, rudimentary plotting, and even some statistics. It costs $5 if you are not a Safari subscriber.</p>

<p><a href='http://oreilly.com/catalog/9780596804787'>Data Mashups in R</a></p>
