Follow the steps:

  • Start Atom
  • Select menu item “View -> Toggle Command Palette”
  • Search for “clone”
  • Select “GitHub: Clone”
  • Enter the URL of the GitHub project you want to clone
  • Click “Clone”

To know the URL to use, go to https://github.com, navigate to the repository you want to clone, click the “Clone or Download” button and copy the URL. You can choose between HTTPS and SSH, I would generally advise to use SSH, provided you have your SSH private key installed.