First of all, I use Scapple as a tool to organise my thoughts, brainstorm, and plan my work (background on the figure above).
Most of the data I work with comes from structured surveys. The original raw data is usually entered and cleaned in Excel - primarily because virtually everybody knows how to work with Excel. Once the data is cleaned and ready to be analysed, I export them to .
I have been using GitHub to collaborate/share data analysis (and a bit of writeup) with my co-authors/collaborators for the last year or so. As most journals now require (or at the very least recommend) submitting original data used in the analysis, alongside the relevant scripts/codes, during the manuscript submission process, I thought it was easiest simply to submit the persistent link to the GitHub repository containing all the data and the scripts/codes used in the analysis and visualisation as part of the manuscript submission.