BMI206: Statistical Methods
OVERVIEW – SYLLABUS – READING – LABS – TUTORIALS – PROJECT
Syllabus
All class meetings will be 9:30-10:30am unless otherwise specified. BH=Byers Hall, GH=Genentech Hall, MH=Mission Hall, RH=Rock Hall
| Date / Location | Topic | Instructor | Materials |
|---|---|---|---|
| Oct 7 1:00-3:00 GH-S271 |
Pre-requisite review (BMI) | TAs | Online course 1.1-1.4, 2.1, 3.1-3.3 Slides-Statistics Background |
| Oct 9 1:00-3:00 GH-S261 |
Pre-requisite review (BMI) | TAs | Online course 2.1, 4.1, 4.2, 5.1-5.4 Slides-Statistics Background |
| Oct 10 1:00-3:00 GH-S271 |
Pre-requisite review (BMI) | TAs | Online course 2.1, 4.3, 6.1, 7.1, 8.1 Slides-Statistics Background |
| Oct 11 1:00-3:00 GH-S271 |
Pre-requisite review (BMI) | TAs | MBoC Tutorial |
| Oct 14 BH-413 |
Discussion: Welcome Board work: Linear models |
Pollard | Video-Overview Slides-Overview Video-Linear Models Slides-Linear Models |
| Oct 15 BH-413 |
Coding: Model selection | Pollard | Video-Associations Slides-Associations Video-Model Selection Slides-Model Selection Code |
| Oct 16 RH-102 |
Paper: Polygenic risk scores across ancestries | Pollard/TAs | Prepare for paper discussion |
| Oct 17 MH-2100 |
Lab: Modeling genetic associations | Pollard/TAs | Download lab files Install R Set up / test Jupyter notebooks See Tutorials for help |
| Oct 21 MH-1407 |
Board work: Categorical data | Capra | Video-Categorical Data Slides-Categorical Data Notes-Study Designs Notes-Count Distributions |
| Oct 22 GH-S261 |
Coding: Resampling methods | Capra | Video-Resampling Methods Slides-Resampling Methods Code |
| Oct 23 GH-S261 |
Paper: Gene set enrichment | Capra/TAs | Prepare for paper discussion |
| Oct 24 BH-215 |
Lab: Genomic enrichment tests | Capra/TAs | Download lab files |
| Oct 28 BH-215 |
Board work: Generalized linear models | Pollard | Video-GLMs Slides-GLMs |
| Oct 29 BH-215 |
Coding: Performance evaluation, fitting GLMs | Pollard | Code |
| Oct 30 BH-215 |
Paper: Machine learning pitfalls | Pollard/TAs | Prepare for paper discussion Review optional tutorial |
| Oct 31 BH-215 |
Discussion: Exploratory data analysis | Quigley | Slides-Exploratory Data Analysis Ch7: EDA from R for Data Science EDA: data visualization or torture? |
| Nov 4 BH-215 |
QBC Retreat: No class | – | – |
| Nov 5 BH-215 |
QBC Retreat: No class | – | – |
| Nov 6 BH-215 |
QBC Retreat: No class | – | – |
| Nov 7 BH-215 |
Lab: Exploratory Data Analysis | Quigley/TAs | Download lab files |
| Nov 11 | Holiday: No class | – | – |
| Nov 12 GH-106 |
Board: Multiple hypothesis testing | Capra | Video-Multiple Testing Slides-Multiple Testing Slides-Adjusting P-values Slides-More Multiple Testing |
| Nov 13 BH-215 |
Coding: Multiple hypothesis testing | Capra | Code |
| Nov 14 BH-215 |
Paper: Genomic enrichments with footprints | Capra/TAs | Prepare for paper discussion |
| Nov 18 BH-215 |
Discussion: Network statistics | Baranzini | Video-Networks1 Video-Networks2 Slides-Graph Theory Slides-Biological Networks |
| Nov 19 RH-102 |
Coding: Cytoscape | Baranzini | Install and test Cytoscape Install and test packages |
| Nov 20 BH-215 |
Paper: Metabolic networks | Baranzini/TAs | Prepare for paper discussion |
| Nov 21 BH-215 |
Lab: Network analysis | Baranzini/TAs | Download lab files |
| Nov 25 BH-215 |
PRESENTATIONS | Groups 1-2 | |
| Nov 26 BH-215 |
PRESENTATIONS | Groups 3-4 | |
| Nov 27 BH-215 |
PRESENTATIONS | Group 5 | |
| Nov 28 | Holiday: No class | ||
| Dec 2 BH-215 |
Board: Dimension reduction, PCA, t-SNE | Ntranos | Video-Distances Slides-Distances Video-Dimension Reduction Slides-Dimension Reduction Slides-PCA |
| Dec 3 BH-215 |
Coding: Visualizing single-cell clusters | Ntranos | Video-Clustering Slides-Clustering R Code Python Notebook |
| Dec 4 GH-S261 |
Paper: Performing dimension reduction | Ntranos/TAs | Prepare for paper discussion |
| Dec 5 GH-S261 |
Lab: Single-cell genomics | Ntranos/TAs | Download lab files |
| Dec 9 BH-215 |
PRESENTATIONS | ||
| Dec 10 MH-2100 |
PRESENTATIONS | ||
| Dec 11 MH-2100 |
PRESENTATIONS | ||
| Dec 12 MH-2100 |
PRESENTATIONS (if needed) |