Labs content for 2017 & 2018 QMUL MSc Bioinformatics BIO782P (Stats & Bioinformatics) module. These lectures and labs include content authored by Rob Knell (2016) where so marked.
| Day | Date | Lecture | Lab | Goals | Assessment |
|---|---|---|---|---|---|
| 1 | Monday 5th November 2018 | Introduction: Statistics and Bioinformatics (R. Knell, J. Parker) | Introduction to R (R. Knell, J. Parker) | Why bioinformatics is statistical; How to use R; Basic exploratory analyses | (CWK1 5%) Simply plot data |
| 2 | Tuesday 6th November 2018 | Basic statistics (R. Knell, J. Parker) | Chi-squared, Student T (R. Knell, J. Parker) | Simple summary measures | (CWK1 5%) Mean; median; contingency tables; difference statistics and Cis |
| 3 | Weds 7th November 2018 | ANOVA and LMs (R. Knell, J. Parker) | ANOVA and LMs (R. Knell, J. Parker) | ANOVA, regression | (CWK1 20%) Anova, regression |
| 4 | Thursday 8th November 2018 | General linear models (R. Knell, J. Parker) | GLM I (R. Knell, J. Parker) | GLMs, error, interactions | (CWK1 20%) GLMs |
| 5 | Friday 9th November 2018 | More GLMs: Selection, experimental design, assumptions (R. Knell, J. Parker) | GLM II (R. Knell, J. Parker) | Model selection | (CWK1 50%) Appropriate selection, main assessment |
| 6 | Monday 12th November 2018 | What is a model? NOTE: 1000-1100 | Simulation; phylogenetics | Modelling context | (CWK2 50%) Simulation |
| 7 | Tuesday 13th November 2018 | Beyond GLMs | Models & simulation (Pt. II) | Beyond GLMs in para space | None |
| 8 | Wednesday 14th November 2018 | Big data bioinformatics | Regex; Group project | Issues in big data (reproducibility; FDR; power/effect size; distributions) | None |
| 9 | Thursday 15th November 2018 | The toolbox | Docker, grids and the cloud (pt. I) NOTE: 1230-1500 Crick Lecture: Michael Levine, Princeton (optional) NOTE: 1600, Crick Inst. | Where to find more tools/resources. Architectures | (CWK2 50%) Dockerfile |
| 10 | Friday 16th November 2018 | Looking further | Docker, grids and the cloud (pt. II); Open Help Session NOTE: 1300-1500 "My favourite package" symposium NOTE: 1600-1700, Queen's Building. Refreshments after. | Wider context | None / opportunity for troubleshooting |