BMI206: Statistical Methods
OVERVIEW – SYLLABUS – READING – LABS – TUTORIALS – PROJECT
Syllabus
All class meetings will be 9:30-10:30am in MH-2103 unless otherwise indicated.
| Date | Topic | Instructor | Materials |
|---|---|---|---|
| Sep 26 | Pre-requisite review (BMI) | TAs | Online course 1.1-1.4, 2.1, 3.1-3.3 Slides-Statistics Background |
| Sep 27 | Pre-requisite review (BMI) | TAs | Online course 2.1, 4.1, 4.2, 5.1-5.4 Slides-Statistics Background |
| Sep 28 | Pre-requisite review (BMI) | TAs | Online course 2.1, 4.3, 6.1, 7.1, 8.1 Slides-Statistics Background |
| Sep 30 | Pre-requisite review (BMI) | TAs | MBoC Tutorial |
| Oct 10 | Discussion: Welcome Board work: Linear models |
Pollard | Video-Overview Slides-Overview Video-Linear Models Slides-Linear Models |
| Oct 11 | Coding: Model selection | Pollard | Video-Associations Slides-Associations Video-Model Selection Slides-Model Selection Code |
| Oct 12 | Paper: Polygenic risk scores across ancestries | Pollard/TAs | Prepare for paper discussion |
| Oct 13 | Lab: Modeling genetic associations | Pollard/TAs | Download lab files Install R Set up / test Jupyter notebooks See Tutorials for help |
| Oct 17 | Board work: Categorical data | Capra | Video-Categorical Data Slides-Categorical Data Notes-Study Designs Notes-Count Distributions |
| Oct 18 (In HD-160) |
Coding: Resampling methods | Capra | Video-Resampling Methods Slides-Resampling Methods Code |
| Oct 19 (In HD-160) |
Paper: Gene set enrichment | Capra/TAs | Prepare for paper discussion |
| Oct 20 | Lab: Genomic enrichment tests | TAs | Download lab files |
| Oct 24 | Board work: Generalized linear models | Pollard | Video-GLMs Slides-GLMs |
| Oct 25 | Coding: Performance evaluation, fitting GLMs | Pollard | Code |
| Oct 26 | Paper: Machine learning pitfalls | Pollard/TAs | Prepare for paper discussion |
| Oct 27 | Discussion: Projects Optional: ML Pitfalls tutorial |
Pollard/TAs | Review optional tutorial |
| Oct 31 | Board: Multiple hypothesis testing | Capra | Video-Multiple Testing Slides-Multiple Testing Slides-Adjusting P-values |
| Nov 1 | Coding: Multiple hypothesis testing | Capra | Code |
| Nov 2 | Paper: Genomic enrichments with footprints | Capra/TAs | Prepare for paper discussion |
| Nov 3 | Discussion: Exploratory Data Analysis | Quigley | Slides-Exploratory Data Analysis Ch7: EDA from R for Data Science EDA: data visualization or torture? |
| Nov 7 | QBC Retreat: No class | – | – |
| Nov 8 | QBC Retreat: No class | – | – |
| Nov 9 | QBC Retreat: No class | – | – |
| Nov 10 | Lab: Exploratory Data Analysis | TAs | Download lab files |
| Nov 14 | Discussion: Network statistics | Baranzini | Video-Networks1 Video-Networks2 Slides-Graph Theory Slides-Biological Networks |
| Nov 15 | Coding: Cytoscape | Baranzini | Install and test Cytoscape Install and test packages |
| Nov 16 | Paper: Metabolic networks | Baranzini/TAs | Prepare for paper discussion |
| Nov 17 | Lab: Network analysis | Baranzini/TAs | Download lab files |
| Nov 21 | PRESENTATIONS | Groups 1-2 | |
| Nov 22 | PRESENTATIONS | Groups 3-4 | |
| Nov 23 | PRESENTATIONS | Groups 5-6 | |
| Nov 24 | HOLIDAY – no class | ||
| Nov 28 | Board: Dimension reduction, PCA, t-SNE | Ntranos | Video-Distances Slides-Distances Video-Dimension Reduction Slides-Dimension Reduction Slides-PCA |
| Nov 29 | Coding: Visualizing single-cell clusters | Ntranos | Video-Clustering Slides-Clustering R Code Python Notebook |
| Nov 30 | Paper: Performing dimension reduction | Ntranos/TAs | Prepare for paper discussion |
| Dec 1 | Lab: Single-cell genomics | Ntranos/TAs | Download lab files |
| Dec 5 | PRESENTATIONS | ||
| Dec 6 | PRESENTATIONS | ||
| Dec 7 | PRESENTATIONS | ||
| Dec 8 | PRESENTATIONS |