Where does R fit into the big picture of bioinformatics?

In our article titled A beginner’s guide to Bioinformatics – part I, we divided bioinformatics skills into five layers. Using R falls into layer 3, which means you mastered layer 1 and are very comfortable with using the web (NCBI BLAST, EBI tools, etc.) for analysis of genomic data. Also, you are able to install and run programs like BLAST, Clustal, Bowtie or Trinity in your local machine (layer 2). Using R needs a bit more skills than installing and running packaged programs, because R also has its own programming language. However, do not let that demoralize you. R language is far easier than PERL or python. R is the easiest of all layer 3 applications, and it will allow you to do many powerful tasks at the cost of little learning. The purpose of this article is not to have ‘yet another’ introductory tutorial for R, but to guide you through existing online resources to get started. The web is full of excellent introductory articles created by others, and I will refer to the easiest ones that I like the most. I also linked other tutorials and important R sites on the right sidebar, and will continue to add suitable links in the future. Please follow these steps to use R -