NGS Data Analysis With R

This one-day hands-on workshop will introduce users of the R software environment to the specific skills and applications used in the analysis next-generation sequencing (NGS) data. Practical exercises will include quality control and pre-processing of data for differential gene expression, and linking genomic information to external public datasets.

Course Outline

During this course you will learn about;

  • Importing and parse FASTQ sequence files into R
  • Carry out standard QC tests on RNA-Seq datasets
  • Use the limma-voom R package to produce lists of differentially expressed genes between pairs of samples
  • Identify over-represented gene ontology categories in gene lists using the GOStats package

Recommended Participants

NGS data analysis using R is designed for bench scientists, PhD students and early career postdoctoral researchers who are looking to use R for RNA expression analysis. Prior expertise with R and the command line interface is required, to a level equivalent of that provided by a one-day  “Introduction to R” workshop. This workshop is only open to medical researchers in NSW or ACT based organisations.


  • Dr Stephen Rudd, QFAB
  • Dr Diego Barneche, Macquarie University
City Location Date Cost
Sydney EMC Building, MQ 22 May 2015 $165.00 (including GST)

Draft Program

Time Topic
Welcome and RStudio set-up
Data processing and normalisation
10:30 Morning Tea
11:00 NGS data exploration Mapping NGS reads to a reference genome Quality Control from mapped read counts
12:30 Lunch
13:30 Differential expression Gene annotation with BioMart
15:00 Afternoon Tea
Gene set enrichment analysis
Discussion (experimental design, other NGS data types…)
17:00 Final wrap-up and close

Registration and Payment

Places are strictly limited to 25 participants due to the practical component of this course. To manage the high demand, all workshop applicants are subject to a selection process and MUST complete the online application form to be considered for a place. Applicants must meet the requirements to be considered for this workshop. The application period closes 27th of April 2015. Successful applicants will be notified no later than 30th of April 2015. The workshop fee of $165 (including GST) covers course material, computer access, lunch and refreshments. Payment can be made by cheque, EFT or credit card.


For further information contact Andrew Gilbert at

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