Additional Readings

Reproducible research

• Best Practices for Scientific Computing
• Ten Simple Rules for Reproducible Computational Research
• Reproducible Research, Keith A. Baggerly and Donald A. Berry
• Publish your computer code: it is good enough
• Implementing Reproducible Research
• State of the Art: Reproducibility in Artificial Intelligence
• Show Your Work: Improved Reporting of Experimental Results
• A statistical definition for reproducibility and replicability
• What does research reproducibility mean?
• Reproducible Research in Computational Science

Text editors

• 13 Best Text Editors to Speed up Your Workflow
• Atom
  • Atom Keyboard Shortcuts
  • I didn’t know Atom could do that!
  • Atom Flight Manual
• Sublime Text
  • Sublime Text 3 Cheat Sheet
  • 7 shortcuts of a highly effective Sublime Text user
  • Sublime Text Tutorial
  • Putting a WSL Terminal in Sublime Text
• Notepad++
  • Notepad++ cheatsheet
  • User manual
• vim
  • INFO 550 vim survival guide
  • Vim Tips Wiki
  • Popular vim commands
  • vim tutorial
  • Learn vim For the Last Time: A Tutorial and Primer
  • Vim for People Who Think Things Like Vim Are Weird and Hard
  • vim cheatsheet
• emacs
  • Emacs Keys Basics
  • Emacs tutorial (video)
• micro
• VSCode
  • R and VSCode

Command line

• Install Xcode Command Line Tools for Mac
• Cygwin
• Survival guide for Unix newbies
• Settling into Unix
• Shell programming with bash: by example, by counter-example
• Some Essential Unix Commands
• bash FAQ
• Command line murder mystery
• Tutorial video: How to Run Linux/Bash on Windows 10 Using Windows Subsystem for Linux
• Bash tutorial videos
• Using Brew on Windows 10 with Windows Subsystem for Linux

R Markdown

• Installing rmarkdown on WSL
• R Markdown: The Definitive Guide
• Markdown cheat sheet
• R Markdown Tutorial
• R Markdown Cheat Sheet
• knitr code chunk options
• Math in R Markdown
• Creating Tables in R Markdown
• bookdown: Authoring Books and Technical Documents with R Markdown
• R Markdown chapter in R for Data Science
• R Markdown formats chapter in R for Data Science

git and GitHub

• Happy Git and GitHub for the useR
• Oh Sh*t, Git!?!
• Connecting to GitHub with ssh
• Configuring ssh credentials for GitHub
• Another video illustrating connecting to GitHub with ssh
• Karl Broman’s git/github guide
• Pro Git
• Software carpentry notes on git
• Git can facilitate greater reproducibility and increased transparency in science
• Intro to Git for Scientists
• git - the simple guide
• Resources to learn Git
• Github Tutorial
• Git Handbook

GNU Makefiles

• GNU Make home page
• Software carpentry’s Make tutorial
• Karl Broman’s minimal make
• make manual
• GNU Make for Reproducible Data Analysis
• Makefiles for R/LaTeX projects
• Example Makefile for R package
• Managing Projects with GNU Make

Project organization

• Tidy Data
• A Quick Guide to Organizing Computational Biology Projects
• Some Simple Guidelines for Effective Data Management
• Nine simple ways to make it easier to (re)use your data
• Stanford library best practices for file naming
• Stanford library guide to metadata
• here R package

Coding Style

• Software carpentry: Creating R Functions
• R for Data Science: Functions
• DataCamp: A Tutorial on Using Functions in R!
• Code and Data for the Social Sciences: A Practitioner’s Guide
• Best Practices for Scientific Computing
• tidyverse style guide
• The Elements of Programming Style
• The Practice of Programming
• Good Enough Practices for Scientific Computing
• 10 tips for writing cleaner code
• 15 Rules for Writing Quality Code
• Best Practices for Writing R Code

R packages

• Hadley Wickham’s R packages book
• Jeff Leek’s R package tutorial
• Karl Broman’s R package primer
• Jenny Bryan’s Write your first R package
• CRAN R package tutorial
• pkgdown: Make pretty websites for your packages
• roxygen2 vignette
• testthat package
• assertthat package
• Pick a license, any license
• roxygen2 documentation

Docker

• Install Docker
• What is Docker?
• Docker Documentation
• Docker Tutorial
• List of Docker Resources
• Play With Docker in Your Browser
• Dockerfile cheat sheet
• Configure Windows Subsystem for Linux with Docker
• R Docker tutorial
• An Introduction to Docker for R Users
• Using R via rocker

Python

• Install Anaconda
• Anaconda Package Management
• A Comprehensive Look at Basic Python
• A Brief Intro to Pandas
• Code Academy python courses
• Google’s python class
• A byte of python
• tuts+: The best way to learn python
• Software Carpentry: Programming with Python

Jupyter Notebooks

• Jupyter Notebooks Docs
• Try Jupyter in Browser
• Basic Tutorial
• Video Tutorial
• IRkernel Docs
• IRDisplay Docs
• Ipython Magics Docs
• Ipython Widgets Docs
• R Plotly Tutorial
• rpy2 Tutorial
• Google Colab

AWS

• Install awscli (version 2)
• Configuring awscli
• High level s3 awscli commands