Timetable

  • Lectures
  • Monday 9:10am - 10:00am, Ingkarni Wardli, Room B17
  • Practicals
  • Wednesday 9:10am - 11:00am, Johnson Building, Room 111
  • Friday 9:10am - 11:00am, Johnson Building, Room 111

Lectures for this course are held on a Monday, and will clash with two Public Holidays in Semester 1.

  1. Week 2, March 9th, Adelaide Cup Day: No Lecture in Week 2
  2. Week 13, June 7th, Queenโ€™s Birthday: An alternative lecture time may be found for this week. This will be announced closer to the date.
Week Week Starting Lecture Practical
1 2020-03-02 Introduction (Stephen Pederson) Introduction to R and rmarkdown
Manipulating Text in R
2 2020-03-09 Adelaide Cup Day (No Lecture) Using the tidyverse
Plotting Data with the tidyverse
3 2020-03-16 Early Transcriptomic Techniques (Stephen Pederson) Data Types in R
Additional Visualisation
4 2020-03-23 Microarrays and Statistics for Quantification (Stephen Pederson) The Bioconductor Project
Genomic Ranges
5 2020-03-30 Statistics For Transcriptomics (Stephen Pederson) Basic Statistics in R
Differential Expression
6 2020-04-06 RNA-Seq (Zhipeng Qu) Using Limma For Differential Expression
2020-04-13 Mid-Semester Break (No Lecture)
2020-04-20 Mid-Semester Break (No Lecture)
7 2020-04-27 Alignment and Quantification (Zhipeng Qu) More Complex Designs
More Complex Designs (2)
8 2020-05-04 Statistics for RNA-Seq (Stephen Pederson) Alignments and Visualisation
Alignments and Visualisation
9 2020-05-11 Enrichment Analysis (Stephen Pederson) Differential Expression Using edgeR
Enrichment Strategies
10 2020-05-18 Network Analysis (Zhipeng Qu) WGCNA_part1
WGCNA_part2
11 2020-05-25 Single Cell RNA-Seq (Stephen Pederson) scRNA
scRNA
12 2020-06-01 Transcriptome Assembly (Terry Bertozzi) Using StringTie to Define New Transcripts
Assignment and Project Questions
13 2020-06-07 Cancer Applications (Dan Thomas)

Assessments

Assessment Tasks

Assessment Topic Due Date Solutions
Assessment 1 Introductory Work 2020-03-24 Assessment 1 Solutions
Assessment 2 Gene Expression 2020-04-09 Assessment 2 Solutions
Assessment 3 Differential Analysis 2020-05-12 Assessment 3 Solutions
Assessment 4 Enrichment Analysis 2020-05-26 Assessment 4 Solutions
Assessment 5 WGCNA and scRNA 2020-06-09 Assessment 5 Solutions
Assessment 6 Transcriptome Assembly 2020-06-19 Assessment 6 Solutions

Major Project

For the postgraduate students, an additional Major Project is included as part of your curriculum. The details of this project are available here

Assessment Checklist

Have you:

  • Answered all the questions?
  • Followed naming conventions for Assessments?
  • Checked that you have not breached the Academic Honesty Policy.
  • Identified the work as yours?
  • Emails should have the course and assessment task names.
  • Documents should be named with your name, the course name and the assessment task.
  • Printed documents should have you name and the course and assessment task in the text/footer/header.
  • Used appropriate electronic communication with assessors?
  • Emails should have a meaningful subject.
  • Handed in the assignment before the due time (see MyUni)?