Links

RStudio
ggplot2
Cookbook for R
Quick-R
swirl
Coursera R Courses
Shiny
Microsoft R Open

Jupyter Notebook
PyCharm
Rodeo: A Native Python IDE
Anaconda
ggplot
seaborn
A Byte of Python
Codeacademy
Data Analysis Using NumPy and Pandas
Coursera Python Courses
Python for R Users
Learn Python in one video

MATLAB Cookbook
Coursera MATLAB Course

Bayesian data analysis

Stan
Doing Bayesian Data Analysis
Statistical Rethinking

fMRI data analysis

SPM
bspmview
Mango
CONN
BrainNet Viewer
gPPI Toolbox
acpcdetect
Neurosynth
Nipype
C-PAC
Nilearn
NIPY
Coursera fMRI courses
UCLA Advanced Neuroimaging Summer program [lecture videos]

Computation modeling (a.k.a. cognitive modeling)

Cognitive Modeling
Bayesian Cognitive Modeling
Reinforcement learning tutorial PDFs
hBayesDM
TAPAS
VBA toolbox

Miscellaneous

Glip
Slack
Making scientific writing painless
Writing in the Science
Expresso
Why pursue (or not pursue) a PhD?
PhD Comics
A tutorial on Git