R in a Nutshell

Where to Go Next

This chapter just scratches the surface of the tools available through Bioconductor; there are dozens of packages available on Bioconductor for doing different types of analysis. The best place to start is the Bioconductor website: http://www.bioconductor.org.

Here are some suggestions for learning more about this project and how to use the Bioconductor tools.

Resources Outside Bioconductor

If you are working with genetic data, there are a variety of R packages outside Bioconductor that you might find useful. See http://cran.r-project.org/web/views/Genetics.html for more information.

Vignettes

In Getting Help, I introduced vignettes. There is at least one vignette for every package in Bioconductor. For example, let’s attach the affy package and look at the available vignettes:

> library(affy)
> vignette(all=FALSE)

This shows the following list of available vignettes (from affy and Biobase):

Vignettes in package ‘affy’: affy 1. Primer (source, pdf) builtinMethods 2. Built-in Processing Methods (source, pdf) customMethods 3. Custom Processing Methods (source, pdf) vim 4. Import Methods (source, pdf) Vignettes in package ‘Biobase’: BiobaseDevelopment Notes for eSet developers (source, pdf) Bioconductor Bioconductor Overview (source, pdf) ExpressionSetIntroduction An introduction to Biobase and ExpressionSets (source, pdf) HowTo Notes for writing introductory 'how to' documents (source, pdf) Qviews quick views of eSet instances (source, pdf) esApply esApply Introduction (source, ...