Monash University, Clayton Campus
Nov 30, 2015 & Dec 3, 2015
10:00 am - 5:00 pm
Instructors: Roxane Legaie, Stuart Archer, Haroon Naeem, Paul Harrison, Steve Androulakis
Helpers: Andrew Pattison, Adele Barugahare, David Powell, Jason Rigby, Grischa Meyer
RNASeq using R
The Monash Bioinformatics Platform want to help make introductory bioinformatic approaches part of the research landscape in Biomedicine. To do this, a foundation level of expertise amongst as many researchers as possible is an important step forward. The platform will then be available to facilitate this work as well as develop more advanced bioinformatic projects with our researchers.
We are running a two day hands-on workshop with a focus on enabling researchers to be able to analyse RNASeq (next-gen sequencing) data.
- Day 1, we will begin by teaching an introduction to programming using the R language.
- Day 2 will focus on using this knowledge to perform bioinformatic data analysis of some RNASeq data.
The workshop will be taught in a similar style to Software Carpentry workshops. Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: The course is aimed at graduate students and other researchers.
Where: E365 Menzies Building, 20 Chancellor's Walk (lvl3 East wing). Get directions with OpenStreetMap or Google Maps.
Requirements:A link to RStudio will be provided before the workshop. No setup is required. All tools and data will be accessible through your internet browser.
Contact: Please mail steve.androulakis@monash.edu for more information.
Schedule
Day 1 (Programming in R)
| 10:00 | Welcome and setup |
| 10:30 | Intro to R |
| 12:00 | Lunch break |
| 13:00 | Intro to R |
| 14:30 | Coffee |
| 16:30 | Wrap-up |
Day 2 (RNASeq using R)
| 10:00 | Setup and introduction |
| 10:30 | RNASeq using R |
| 12:00 | Lunch break |
| 13:00 | RNASeq using R |
| 14:30 | Coffee |
| 16:30 | Wrap-up |
Etherpad: https://public.etherpad-mozilla.org/p/2015-09-28-rbioinformatics.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Syllabus
This is subject to change!
Programming in R
- Working with vectors and data frames
- Reading and plotting data
- Creating and using functions
- Loops and conditionals
- Reference...
Day 2 (RNASeq using R)
- Intro to RNAseq data
- Quality control and mapping of RNAseq data with R
- Differential expression analysis with R
- Creating plots for differential expression analysis with R
Setup
To participate in this workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
R
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Connect to RStudio
A link to RStudio will be provided before the workshop. No setup is required. All tools and data will be accessible through your internet browser.