Go to a git repo that you would like to clone, for example, https://github.com/bensutherland/fasta_SNP_extraction
Click the green button 'Clone or download', and click 'Open in Desktop'
This will open https://desktop.github.com/
Click the button 'Download for Windows (64 Bit)'
This will download a setup exe file to your Downloads folder 'GitHubDesktopSetup.exe' Run this executable.
A window should pop up stating "Welcome to GitHub Desktop". Sign in to your account.
To start, click one of your repositories and then click the blue button: 'Clone <your_name/your_repo>' By default, your repos will clone into "C:\Users<your_account>\Documents\GitHub"
Now you can either put files into the directory specified above, e.g. into folders within the repo as instructed by the README, or you can open the scripts through R for example.
Any changes that you make to the repo are able to be pushed to your master by using the GitHub desktop application.
Happy Git'ing!