I found Statistical Methods for the Analysis of Biomedical Data by Robert Woolson and William C Clarke helpful both for understanding introductory biostatistics and for supplying SAS code to implement the techniques described.
There are a few good books on Biostatistics using R, in the internet, I'd recommend:
1) Dalgaard P. (2008). Introductory Statistics with R. 2nd Ed. Springer. http://www.academia.dk/BiologiskAntropologi/Epidemiologi/PDF/Introductory_Statistics_with_R__2nd_ed.pdf.
2) Logan M. (2010). Biostatistical Design and Analysis Using R. A Practical Guide. Wiley-Blackwell. http://www.ievbras.ru/ecostat/Kiril/R/Biblio/R_eng/Logan Biostatistical.pdf.
3) Seefeld K. and Linder E. (2007). Statistics Using R with Biological Examples. University of New Hampshire, Durham, NH. Department of Mathematics & Statistics. https://cran.r-project.org/doc/contrib/Seefeld_StatsRBio.pdf.
And of course the classic on the topic is 4) Sokal R.R & Rohlf F.J. (1969). Introduction to Biostatistics. 2nd Ed. Dover Publications Inc. Mineola New York. This book is outdated on the programming side but still good and very cheap!
I have used Matlab, R, SAS, Stata, and SPSS. Personally I don't like Matlab because the modules to perform certain analyses are quite expensive and they are not forthcoming with the methods used to derive at the answers it outputs. It's sort of a black box. SPSS I find too simplistic and in order to really do much beyond basic statistics you'll have to pay and pay. SAS, like SPSS requires you to pay a yearly licensing fee but it is probably the best software for managing and merging very large datasets. The programming language is quite old which I suppose might be a strength for someone repeating a study years later. Stata is quite simple to use but I believe very powerful especially for epidemiologists and biostatisticians. Though this article mentions time-series abilities of SAS, it was Stata that incorporated time-series long before SAS did. R is the only free program but has the potential to be the most powerful with a wealth of user-written programs but it does have the steepest learning curve of the bunch. Stata also makes use of user-written programs for atypical analyses but much less so than R. SAS users contribute macros which are similar in concept but typically not as user friendly. Lastly, while SAS is able to handle very large datasets, R and Stata are capable of this provided your computer has enough RAM installed. It's a tough decision.