Lecture slides

Homework: DataCamp Intro to R course (~2hrs) - due before the start of class on Feb 13th.

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, and each student will set-up their own laptop to be a powerful,stand-alone bioinformatics workstation.

Software

Download and install the following software before class (except Kallisto)

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 - For mac folks

Cygwin - For PC folks…to 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. We will install this program together in class