NGS Data Analysis Using R/Bioconductor
Thur, March 12, 2015
Instructor: Thomas Girke

Schedule & Teaching Material

08:30-10:00 AM - Introduction to R/Bioconductor    [ Slides ]   [ Exercises ]   [ Manual ] 
10:00-10:15 AM - Coffee Break
10:15-11:45 AM - Basics on Analyzing Next Generation Sequencing Data (Part I)    [ Slides ]   [ Exercises ]   [ Manual ] 
11:45-12:45 PM - Lunch Break
12:45-02:00 PM - Basics on Analyzing Next Generation Sequencing Data (Part II)
02:00-02:15 PM - Coffe Break
02:15-05:00 PM - Analysis of RNA-Seq Data    [ Slides ]   [ Exercises ]   [ Manual ] 
 
Laptop and Software Requirements

Laptop Requirements
  • Users are expected to bring a laptop with a functional wireless connection and a recent internet browser version (e.g. Firefox, Chrome or Safari) preinstalled. Tablet computers with mobile operating systems are not suitable for running the required software. Wireless guest accounts will be provided by the organizers. Also, don't forget to bring a power supply for your laptop to run it for an entire day!
  • If your laptop has special firewall settings (e.g. company owned laptops), then please make sure you know how to administer your firewall settings (e.g. lower restrictions or turn on/off). 
  • In addition, please follow the software install and data download instructions for this event as outlined below. 
Data Downloads
  • Please download the sample data required for the RNA-Seq module of this event from here. 
Software Installs
  • Install latest R Version 3.1.2 (or 3.1.3) from here: http://www.r-project.org/
  • Next, install RStudio Desktop from here: http://www.rstudio.com/products/RStudio/#Desk 
  • Optional install: IGV (Integrative Genomics Viewer) will be used only in one short example (http://www.broadinstitute.org/igv/)
  • OS X users may need to install XQuartz
  • To install the R libraries required for the different course modules, copy & paste the following commands into the R console of RStudio and then execute them by hitting the enter key. Note: the first three lines should be executed line by line!
source("http://bioconductor.org/biocLite.R")
biocLite() # If asked to update hit 'a'
biocLite("BiocUpgrade") # If asked to update hit 'y'
biocVersion() # Note: this should return Bioc Version '3.0' or higher!!
sessionInfo() # Note: this needs to return R Version 3.1.2 or higher!!
install.packages(c("ggplot2", "lattice", "ape"))
biocLite(c("BiocStyle", "ggbio", "ShortRead", "Biostrings", "IRanges", "BSgenome", "rtracklayer", "biomaRt", "Rsamtools", "GenomicRanges", "GenomicAlignments", "DESeq", "DESeq2", "edgeR", "leeBamViews", "GenomicFeatures", "DEXSeq", "BCRANK", "SRAdb", "systemPipeR", "AnnotationDbi", "RCurl", "ape", "XML", "acepack", "seqLogo"))