evolution - Learn Bioconductor the hard way!

I came to analyzing population genetics data from the background of a theoretician and a computer biologist but not with the standard tools that a bioinformatician (or empiricist in population genetics) know of. I have a fairly good knowledge in R and in programming in general.

I am looking for a course/tutorial for learning bioconductor (and other R tools for analyzing genetic data). A course/tutorial that is short, dense and assumes the user has good knowledge in programming. I am happy with both a video or a written tutorial although I would slightly prefer a written tutorial. I typically aim at analyzing data on structured populations such as the average number of pairwise differences among population, or graphing the site frequency spectrum per population, etc..

There are a fair number of such tutorials. Can you please give me recommendations?

Answer

I recommend the DESeq2 tutorial at:

http://www.bioconductor.org/help/workflows/rnaseqGene/

I think this is a good start for you because:

• DESeq2 is a very popular package. You'll learn how exactly a bioinformatician works.


• The workflow starts from alignments, and show you how to connect command-line tools with the R-package



• It shows you how to generate MA plot, PCA plot etc. You'll appreciate how easy to do such things in R.


• Testing for differential gene expression is very important


• You'll learn how R does the programming. For example, in R it's a good idea to create a data set object, and do something like this:

obj <- .... # This is my R-object
obj <- fun1(obj) <- # Function 1 adds information to the object
obj <- fun2(obj) <- # Function 2 adds more information to the object