Git:

• A step-by-step guide to git
• Getting started with git and github
• Using git on the command line

Bash:

• Bash scripting for beginners
• A beginner's guide to shell scripting

R:

• Getting started with R
• R Tutorial
• UZH R Courses
• Zurich R user group
• Wolfgang Viechtbauer's R course
• Wolfgang Viechtbauer's meta-analysis course

Python:

• Getting started with python
• Learning python
• UZH Foundations of programming with python
• UZH Python - data analysis essentials

Matlab:

• Getting started with matlab
• Introduction to programming with matlab
• UZH Introduction to matlab

Emacs:

• A guided tour of emacs
• How I learned to stop worrying and love emacs
• Getting started with org-mode
• Magit: git in emacs

SPM:

• UCL SPM course
• TNU Previous SPM courses
• SPM mailing list

FSL:

• Learning FSL
• Oxford FSL courses

Freesurfer:

• Boston freesurfer course
• Freesurfer tutorial
• Teach yourself freesurfer

AFNI:

• AFNI training bootcamp
• Introduction to AFNI

Computational psychiatry:

• TNU Zurich computational psychiatry course
• Transcontinental computational psychiatry workgroup

Stan:

• The Stan forum
• Stan user guide

Cognitive neuroscience:

• Collection of resources for cognitive neuroscience

RMarkdown:

• Getting started with RMarkdown
• Online website
• User guide

Scientific writing:

• UZH course
• USZ course
• Ten simple rules for structuring papers
• Ten simple rules for writing research papers

• Ten simple rules for making good oral presentations

Journalism:

• Should scientists require copy checking?

Social media:

• Ten simple rules for getting started on Twitter as a scientist

Blogs:

• Slate Star Codex
• Error statistics blog
• Andrew Gelman's blog
• Data colada
• Danielle Navarro's blog
• Tal Yarkoni's blog