(This article was first published on chem-bla-ics, and kindly contributed to R-bloggers)
I just heard that my supervisor's book Chemometrics with RThis book is recommended to all bioinformaticians too: many former colleagues from my old department are now in fact working in bioinformatics (see also this BioStar answer).
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Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).