Bioinformatics Resources

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Resources for Bioinformatics Software Development & Data Analysis

I found myself sending some of the same links over and over again to people who asked questions related to bioinformatics. So it was time to compile all the links in one convenient place!

All of the resources linked below are free unless otherwise noted. This isn’t intended to be an exhaustive list of all the resources available, just some of the ones I have come across and have found useful.

Last updated: 2019-09-05

Table of Contents:

Programming

Python

R

Reproducibility

Project organization

Literate programming

R Markdown

Jupyter

Documentation

Misc. Tools

For git

  • Link your university email to GitHub to get pro/education features.
    • All users (Pro or free) get free unlimited private repositories on GitHub.
  • GitKraken has a nice GUI for interacting with git, GitHub, GitLab, etc. (Note that this is a referral link to be entered to win a Nintendo Switch.)

Editors

etc.

  • Oh My ZSH!: framework for managing your zsh configuration. I switched from bash to zsh because of this and haven’t looked back!
  • docopt: easily create & parse command-line interfaces. Available for Python, R, C++, & more.
  • csvkit: command-line tool for working with and converting to CSV format from Excel, JSON, etc.
  • Hypothesis Python testing module.