DIRT is a directory of digital research tools. The tools are handily classified according to what you want the tool to do; analyze data; organize data; model data; etc. You can also select what kind of data you have and it will offer tools to work with it.
The Programming Historian offers lessons in using tools to analyze and work with data including lessons on Python; R; APIs; digital and web presentation software; and mapping/GIS tools. Lessons range from basic to advanced.