Lecture slides on iCloud

Overview

In the first half of this lecture we’ll discuss the open-source, cross-platform R/bioconductor software and environment that will be used throughout the course, then each student will set-up their own laptop to be a powerful, stand-alone bioinformatics workstation.

Learning objectives

  • Brief overview of the tools we’ll use throughout the course (R/Bioconductor, RStudio, etc.)
  • Set-up your laptop with all the software needed for the course

Software

I’ll walk you through installing the following software

R Programming Language - The only programming language we’ll work with in class.

RStudio - a development environment for the R programming language.

Sublime text editor - a simple but powerful text editor that is ‘code aware’

Visual Studio Code - an alternative to Sublime and an excellent choice for working with scripts outside of RStudio.

XCode developer tools - Only download if running on Mac OS on your laptop.

Cygwin - Only download if running a Windows OS on your laptop. Cygwin will give your system more linux-like capabilities

Kallisto - This is the software we’ll use for mapping raw reads to a reference transcriptome. Detailed instructions for installing and using Kallisto are available on my lab’s SOP site here.


Lecture video

Part 1 - An overview of the software tools we’ll use on our laptops for the course, as well as options for computing hardware.

Part 2 - Installing software and talking about the relationship between R, RStudio and Bioconductor.