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      Bioinformatics: Command Line/R Prerequisites 2020

Home
Introduction
Intro to the Workshop and Core
Schedule
Resources
Zoom help
Slack help
Software and Links
Cheat Sheets
Intro CLI
Logging in
Introduction to the Command Line part 1
Introduction to the Command Line part 2
The cluster and modules
Introduction to Python
Python Part1, Background
Python Part2, Data Types
Python Part2, Solutions
Python Part3, Flow Control
Python Part3, Solutions
Python Part4, Working with Files
Python Part4, Solutions
Advanced CLI
Advanced Command Line
Advanced Challenge Solutions
A Simple Bioinformatics Workflow
Software Installation
Using make and cmake
Using Conda
Getting set up with AWS
AWS Event Engine
Starting and Stopping your AWS Instance
Introduction to R
Introduction to R
Introduction to tidyverse
Organizing, manipulating, and visualizing data in the tidyverse
Advanced R
Linear models in R
ETC
Closing thoughts
Github page
Biocore website

Software and Links

Linux Terminal:

  1. Shell for Windows 10 tutorial
  2. Enable SSH tutorial OR
  3. MobaXterm
  4. PuTTY

File Transfer:

  1. FileZilla
  2. Cyberduck

R and RStudio

  1. R project
  2. RStudio Desktop
    Also see this link if you have trouble installing under Ubuntu

Software

  1. HTStream
  2. Star
  3. Salmon
  4. IGV
  5. MultiQC

Code Editors

  1. Atom editor
  2. Visual Studio Code