Jeff Leek and Roger Peng started their course Advanced Data Science at Johns Hopkins University. It’s meant for JHU students, but you can learn from the weekly course material for free:
The class is not designed to teach a set of statistical methods or packages – there are a ton of awesome classes, books, and tutorials about those things out there! Rather the goal is to help you to organize your thinking around how to combine the things you have learned about statistics, data manipulation, and visualization into complete data analyses that answer important questions about the world around you.
So you know the methods and tools (or how to learn them on your own), but you want to learn more about putting it all together.
Nice. I could probably use a refresher.
You can get the weekly updates here.