Next Generation Data Analysis Marathon

December 5-8, 2014

Overview
This 4-day workshop is for users who want to acquire the skills required to analyze next generation sequence (NGS) and other large-scale data sets independently and in a proficient manner. Most workshop modules will use the data analysis environment R/Bioconductor which is currently the Lingua Franca of data driven research. No prior knowledge of R is required for attending this workshop, but beginners should sign up for the introductory sections on Friday which will provide the basics required for the applied data analysis sections of this event. The last module on Monday afternoon will introduce the web-based NGS data analysis environment Galaxy that requires no special computer knowledge.
Sign-up
To sign up for this event, please visit the sign-up page by clicking the button on the right. Since the event is entirely booked out now, the sign-up page has been disabled! 
http://manuals.bioinformatics.ucr.edu/workshops
Location
Genomics Lecture Hall, UC Riverside [ Map ]
Parking: Participants will need a permit to park on campus. The closest parking lot available for non-UCR participants to park is Lot 6. A dispenser is available in this lot for purchasing daily permits. Here is a map to locate Lot 6 and the Genomics building. 

Schedule

Fri, Dec 5, 2014

09:00-12:00 PM - (1a) Introduction to R (Instructor: Thomas Girke)    [ Slides ]   [ Exercises ]   [ Manual ] 
                             (1b) R Graphics Demo Slides (Instructor: Thomas Girke)    [ Slides ]   [ Exercises ]   [ Manual ] 
12:00-01:00 PM - Lunch Break 
01:00-06:00 PM - (2) Programming in R (Instructor: Thomas Girke)     [ Slides ]   [ Exercises ]   [ Manual ]

Sat, Dec 6, 2014

09:00-12:30 PM - (3) Basics on Analyzing Next Generation Sequencing Data with R/Bioconductor  (Instructor: Thomas Girke)    [ Slides ]   [ Exercises ]   [ Manual ] 
12:30-01:30 PM - Lunch Break
01:30-06:00 PM - (4) Analysis of RNA-Seq Data with R/Bioconductor (Instructor: Thomas Girke)     [ Slides ]   [ Exercises ]   [ Manual ] 

Sun, Dec 7, 2014

09:00-12:30 PM - (5) Analysis of ChIP-Seq Data (Instructor: Thomas Girke)    [ Slides ]   [ Exercises ]   [ Manual ] 
12:30-01:30 PM - Lunch Break
01:30-06:00 PM -  (6) Analysis of SNP/Var-Seq Data (Instructor: Neerja Katiyar)     [ Slides ]   [ Exercises ]   [ Manual ] 

Mon, Dec 8, 2014

09:00-11:00 AM - (7a) Cheminformatics of Drug-like Small Molecules (Instructor: Thomas Girke)     [ Slides ]   [ Exercises ]   [ Manual ]
11:00-12:30 PM - (7b) Analysis of High-Throughput Compound Screens (Instructor: Tyler Backman)     [ Slides ]   [ Exercises ]   [ Manual ]
12:30-01:30 PM - Lunch Break
01:30-05:30 PM - (8) Web-based Analysis of Next Generation Sequence Data (Instructor: Rakesh Kaundal)     [ Slides]   [ Exercises ]   [ Manual ]

Sponsors  

http://www.nsf.gov    http://www.nsf.gov 
 http://www.siliconmechanics.com/
 
http://www.raidinc.com/
        
http://www.rstudio.com/   
http://www.seagate.com/products/enterprise-servers-storage/enterprise-storage-systems/
   
 
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 for non-UCR participants. 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) to allow ssh connections and biocLite installs. 
  • In addition, please follow the software install instructions for each event as outlined below. If you encounter problems, then please email Jordan Hayes (jordan.hayes@ucr.edu) to assist you with the installation.
Software Installs
  • Install latest R Version 3.1.2 from here: http://www.r-project.org/
  • Next, install RStudio from here: http://rstudio.org/ 
  • IGV (Integrative Genomics Viewer) will be used in some parts of the NGS analysis sections: http://www.broadinstitute.org/igv/
  • To install the R libraries required for the different course modules, copy & paste the following commands into the RStudio (or the R) console and execute them with the enter key:
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("BiocUpgrade")
biocVersion() # Note: this should return Bioc Version '3.0' or higher!!
sessionInfo() # Note: this needs to return R Version 3.1.2!!
install.packages(c("ggplot2", "lattice", "ape", "pvclust", "biclust", "modeltools", "som", "flexclust", "cluster", "scatterplot3d", "gplots", "e1071", "kernlab"))
biocLite(c("BiocStyle", "ggbio", "ShortRead", "Biostrings", "IRanges", "BSgenome", "rtracklayer", "biomaRt", "chipseq", "ChIPpeakAnno", "Rsamtools", "BayesPeak", "PICS", "GenomicRanges", "GenomicAlignments", "DESeq", "DESeq2", "edgeR", "leeBamViews", "GenomicFeatures", "DEXSeq", "BCRANK", "VariantAnnotation", "SRAdb", "ChemmineR", "fmcsR", "QuasR", "systemPipeR", "Rbowtie", "AnnotationDbi", "bioassayR", "cellHTS2", "RCurl", "ape","XML", "acepack", "seqLogo"))
biocLite(c("gmapR", "VariantTools"), type="source") # Last two packages are not supported on Windows!