- Software Carpentry A series of courses on many useful scientific software skills. It's great to take the course, but one can also go through the classes or read through the teacher guides.
- MIT's Missing Semester MIT's version of Software Carpentry
- Research Software Engineering with Python A big picture guide through unix, git, team collaboration, testing, provenance, and packaging
- The Turing Way A book on effictive ways to design and support reproducible research. Focuses on coding details as well as guides to building a collaborative and supportive community.
- Good Research Code Handbook by Patrick Mineault
- HPC/Biowulf Bash Course
- Software Carpentry: The Unix Shell
- Cornell Linux Tutorial
- AFNI Unix Introduction
- Lab Guide (Beginner; data analysis focus)
- Coursera specialization by University of Michigan
- Software Carpentry: Programming with Python
- Gael Varoquaux's Programming Guides (Varying difficulties)
- SciPy lecture notes (Varying difficulties)
- Open Tech School iPython (Beginner, notebooks)
- Python String Format by pyformat (Beginner, String Formatting)
- iPython Advanced Documentation (Advanced; reference)
- Full Stack Python (Advanced; process-focused)
- Awesome Python (Reference for Python Frameworks)
- Chris Yeh's Definitive Guide to Python import statements (For people making packages)
- Python for the practicing neuroscientist (more for lower level signal analysis))