I use "R" with "Bioconductor".
First, you need install the "R" on your computer.
To install the "R" and "Bioconductor", please visit the following sites and see the instructions.
The R Project for Statistical Computing
Bioconductor
You will be able to install some packages by using the "Package Installer" on the "R".
To perform your analysis, you only need copy and past the ">" row on your "R" window, and change my data or file name to yours in the row.
When you finish your work, just type "q()" or "CTRL+D".
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I referred to the following books for "R" with "Bioconductor".