Hands-on workshop: Bioconductor / Shiny for genomic analysis

Venue: QUT, Brisbane, Australia

Date: Thursday 3rd November 2016


Prof. Martin Morgan, Roswell Park Cancer Institute, Buffalo, NY, USA

Dr. Paul Harrison, Monash Bioinformatics Platform, Melbourne, Australia

Overview. DNA sequence analysis generates large volumes of data that present challenging bioinformatic and statistical problems. This tutorial introduces established and new Bioconductor packages and workflows for analyzing high-throughput sequence data. The Bioconductor project (http://bioconductor.org) is a widely used collection of over 1,200 R packages for high-throughput genomic analysis. Approaches for efficiently manipulating sequences and alignments and other common work flows will be covered along with the unique statistical challenges associated with 'RNAseq', variant annotation and other experiments. The emphasis is on exploratory analysis, and the analysis of designed experiments. The workshop will touch on the Biostrings, ShortRead, GenomicRanges, VariantAnnotation, and other packages, with short exercises to illustrate the functionality of each package.

The Shiny (http://shiny.rstudio.com) library and web server make it possible to create an interactive interface to R code and graphics. In the second part of this workshop, participants will write a simple genome browser using Shiny, in the process learning the basics of Shiny and how to set up a Shiny application. By the end of the workshop, participants will be able to create their own interactive apps allowing sharing of analyses with collaborators.


  1. Gain overall familiarity with Bioconductor packages for high-throughput sequence analysis, including Bioconductor vignettes and classes.
  2. Obtain experience running bioinformatic workflows for data quality assessment, RNA-seq differential expression, and manipulating variant call format files.
  3. Appreciate the importance of ranges and range-based manipulation for modern genomic analysis.
  4. Learn how to write you own Shiny app for interactive analysis, and collaboration.


Introduction to Bioconductor -- packages and classes

Short work flows - Exploring sequences and alignments

   - RNA-seq: a high-level tour

   - Annotating variants

Shiny -- learn to use Shiny by creating a simple genome browser

Prerequisites. The workshop assumes an intermediate level of familiarity with R, and basic understanding of biological and technological aspects of high-throughput sequence analysis. Participants should come prepared with a modern wireless-enabled laptop and web browser installed.

Intended Audience. This workshop is for professional bioinformaticians and statisticians interested in using R/Bioconductor and Shiny for analysis and comprehension of high-throughput sequence data.




Dr Matt Ritchie, Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Dr Jovana Maksimovic, Murdoch Childrens Research Institute, Melbourne, Australia

Mr Stephen Pederson, Bioinformatics Centre, The University of Adelaide, Adelaide, Australia

The organisers are grateful to AGTA (http://www.agtagenomics.org.au), ABACBS (http://www.abacbs.org/about/and CSL Limited (www.csl.com.au) for their financial support of this meeting.