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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?

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  • $\begingroup$ bioconductor is a source for packages, You can ask for tutorials to bioinformatics packages in bioconductor, those would be the vignettes. But, I don't understand what you mean by tutorials for bioconductor. Of the top of my head if you have population genetics data, then most probably you are dealing with normal distributions. There are statistical packages which are far more robust than most packages on bioconductor. This question is a bit unclear as to what you want to do and what sort of data you have. $\endgroup$ – FoldedChromatin Aug 8 '16 at 9:05
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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

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  • $\begingroup$ I'm not able to fix the format. Can someone help me? $\endgroup$ – SmallChess Aug 3 '16 at 8:16
  • $\begingroup$ I tried to fix the formatting, but the formatting looks bugged. $\endgroup$ – bli Aug 3 '16 at 8:33
  • $\begingroup$ @bli Sorry, I tried to answer the question as best as I could, but I somehow screwed the formatting. $\endgroup$ – SmallChess Aug 3 '16 at 8:34
  • $\begingroup$ I mean, it doesn't seem to be your fault that the formatting is screwed: Normally, 4-space indentation works and it seems to me you did it right. Or maybe code-formatting is not expected to work after listings ? $\endgroup$ – bli Aug 3 '16 at 8:43
  • $\begingroup$ @bli Yeah. I was trying to do code formatting, but I couldn't get it working... $\endgroup$ – SmallChess Aug 3 '16 at 8:44

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