BMI206: Statistical Methods
OVERVIEW – SYLLABUS – READING – LABS – TUTORIALS – PROJECT
Syllabus
All class meetings will be 9:30-10:30am in Byers Hall Room 215 unless otherwise specified.
| Date / Location | Topic | Instructor | Materials |
|---|---|---|---|
| Oct 6 | Pre-requisite review (BMI) | TAs | Online course 1.1-1.4, 2.1, 3.1-3.3 Slides-Statistics Background |
| Oct 7 | Pre-requisite review (BMI) | TAs | Online course 2.1, 4.1, 4.2, 5.1-5.4 Slides-Statistics Background |
| Oct 8 | Pre-requisite review (BMI) | TAs | Online course 2.1, 4.3, 6.1, 7.1, 8.1 Slides-Statistics Background |
| Oct 9 | Pre-requisite review (BMI) | TAs | MBoC Tutorial |
| Oct 13 | Discussion: Welcome Board work: Linear models |
Pollard | Slides-Overview Video-Linear Models Slides-Linear Models |
| Oct 14 | Coding: Model selection | Pollard | Video-Associations Slides-Associations Video-Model Selection Slides-Model Selection Code |
| Oct 15 | Paper: Polygenic risk scores across ancestries | Pollard/TAs | Prepare for paper discussion |
| Oct 16 | Lab: Modeling genetic associations | Pollard/TAs | Download lab files Install R Set up / test Jupyter notebooks See Tutorials for help |
| Oct 20 | Board work: Categorical data | Capra | Video-Categorical Data Slides-Categorical Data Notes-Study Designs Notes-Count Distributions |
| Oct 21 | Coding: Resampling methods | Capra | Video-Resampling Methods Slides-Resampling Methods Code |
| Oct 22 | Paper: Gene set enrichment | Capra/TAs | Prepare for paper discussion |
| Oct 23 | Lab: Genomic enrichment tests | Capra/TAs | Download lab files |
| Oct 27 | Board work: Generalized linear models | Pollard | Video-GLMs Slides-GLMs |
| Oct 28 | Coding: Performance evaluation, fitting GLMs | Pollard | Code |
| Oct 29 | Paper: Machine learning pitfalls | Pollard/TAs | Prepare for paper discussion Review optional tutorial |
| Oct 30 | Projects | Pollard | |
| Nov 3 | QBC Retreat: No class | – | – |
| Nov 4 | QBC Retreat: No class | – | – |
| Nov 5 | Discussion: Exploratory data analysis | Quigley | Slides-Exploratory Data Analysis Ch7: EDA from R for Data Science EDA: data visualization or torture? |
| Nov 6 | Lab: Exploratory Data Analysis | Quigley/TAs | Download lab files |
| Nov 10 | Board: Multiple hypothesis testing | Capra | Video-Multiple Testing Slides-Multiple Testing Slides-Adjusting P-values Slides-More Multiple Testing |
| Nov 11 | Holiday: No class | – | – |
| Nov 12 | Coding: Multiple hypothesis testing | Capra | Code |
| Nov 13 | Paper: Enhancer-Gene maps | Capra/TAs | Prepare for paper discussion |
| Nov 17 | Discussion: Network statistics | Baranzini | Video-Networks1 Video-Networks2 Slides-Graph Theory Slides-Biological Networks |
| Nov 18 | Coding: Cytoscape | Baranzini | Install and test Cytoscape Install and test packages |
| Nov 19 | Paper: Metabolic networks | Baranzini/TAs | Prepare for paper discussion |
| Nov 20 | Lab: Network analysis | Baranzini/TAs | Download lab files |
| Nov 24 | PRESENTATIONS | Groups 1-2 | |
| Nov 25 | PRESENTATIONS | Groups 3-4 | |
| Nov 26 | PRESENTATIONS | Group 5 | |
| Nov 27 | Holiday: No class | ||
| Dec 1 | Board: Dimension reduction, PCA, t-SNE | Ntranos | Video-Distances Slides-Distances Video-Dimension Reduction Slides-Dimension Reduction Slides-PCA |
| Dec 2 | Coding: Visualizing single-cell clusters | Ntranos | Video-Clustering Slides-Clustering R Code Python Notebook |
| Dec 3 | Paper: Performing dimension reduction | Ntranos/TAs | Prepare for paper discussion |
| Dec 4 | Lab: Single-cell genomics | Ntranos/TAs | Download lab files |
| Dec 8 | PRESENTATIONS | ||
| Dec 9 | PRESENTATIONS | ||
| Dec 10 | PRESENTATIONS | ||
| Dec 11 | PRESENTATIONS (if needed) |