This workshop refers to content in the RNA-Seq wiki.
Post your workshop questions here!
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Instructions to setup your laptop can be found here.
Difference Between R and RStudio
RStudio doesn’t know where libraries are installed, when they are not installed through the RStudio package manager. To tell RStudio the location, you can define the path in a startup file. Create a file called .Renviron . Inside there:
R_LIBS=<R Library Path of other installed packages>
That was the problem when students installed things in RStudio at the command line using the R command
… or you could use the package manger to install libraries.
… of scripts in the R editor does not seem to work under Windows. If you want highlighted syntax, use RStudio instead.
Before coming to the workshop read these:
1) R Preparation tutorials: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before.
2) UNIX Preparation tutorials:
3) IGV Tutorial: Review how to use IGV Genome Browser if you have not used this tool before.
- The IGV Tutorial
Instructions can be found here.
- We have set up 32 instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. If you plan on using Linux or Mac OS X, please download this certificate. Otherwise if you plan on using Windows (with Putty and Winscp), please download this certificate.
YouTube Playlist for Recorded Lectures
Module 1 Lab
Module 2 Lab
Module 3 Lab
Module 4 Lab
Keeping Up-to-date with RNA-Seq Analysis Developments
For additional resources, tutorials, future directions, and more please refer to the RNA-seq wiki
Data for the Workshop
Instructions for installing the tools used in the workshops can be found here.