BMI206: Statistical Methods

OVERVIEWSYLLABUSREADING –  LABS – TUTORIALSPROJECT

Syllabus

All class meetings will be 9:30-10:30am in Byers Hall Room BH-313 unless otherwise specified.

Date Topic Instructor Materials
Oct 9 1:30-3:30
BH-513
Pre-requisite review (BMI) TAs Online course 1.1-1.4, 2.1, 3.1-3.3
Slides-Statistics Background
Oct 10 1:30-3:30
BH-513
Pre-requisite review (BMI) TAs Online course 2.1, 4.1, 4.2, 5.1-5.4
Slides-Statistics Background
Oct 11 1:30-3:30
BH-513
Pre-requisite review (BMI) TAs Online course 2.1, 4.3, 6.1, 7.1, 8.1
Slides-Statistics Background
Oct 12 1:30-3:30
BH-513
Pre-requisite review (BMI) TAs MBoC Tutorial
Oct 16 Discussion: Welcome
Board work: Linear models
Pollard Video-Overview
Slides-Overview
Video-Linear Models
Slides-Linear Models
Oct 17 Coding: Model selection Pollard Video-Associations
Slides-Associations
Video-Model Selection
Slides-Model Selection
Code
Oct 18 Paper: Polygenic risk scores across ancestries Pollard/TAs Prepare for paper discussion
Oct 19 Lab: Modeling genetic associations Pollard/TAs Download lab files
Install R
Set up / test Jupyter notebooks
See Tutorials for help
Oct 23 Board work: Categorical data Capra Video-Categorical Data
Slides-Categorical Data
Notes-Study Designs
Notes-Count Distributions
Oct 24 Coding: Resampling methods Capra Video-Resampling Methods
Slides-Resampling Methods
Code
Oct 25 Paper: Gene set enrichment Capra/TAs Prepare for paper discussion
Oct 26 Lab: Genomic enrichment tests Capra/TAs Download lab files
Oct 30 Board work: Generalized linear models Pollard Video-GLMs
Slides-GLMs
Oct 31 Coding: Performance evaluation, fitting GLMs Pollard Code
Nov 1 Paper: Machine learning pitfalls Pollard/TAs Prepare for paper discussion
Review optional tutorial
Nov 2 Discussion: Exploratory data analysis Quigley Slides-Exploratory Data Analysis
Ch7: EDA from R for Data Science
EDA: data visualization or torture?
Nov 6 QBC Retreat: No class
Nov 7 QBC Retreat: No class
Nov 8 QBC Retreat: No class
Nov 9 Lab: Exploratory Data Analysis Quigley/TAs Download lab files
Nov 13 Board: Multiple hypothesis testing Capra Video-Multiple Testing
Slides-Multiple Testing
Slides-Adjusting P-values
Nov 14 Coding: Multiple hypothesis testing Capra Code
Nov 15 Paper: Genomic enrichments with footprints Capra/TAs Prepare for paper discussion
Nov 16 Discussion: Project team meetings TAs
Nov 20 PRESENTATIONS Groups 1-2
Nov 21 PRESENTATIONS Groups 3-4
Nov 22 PRESENTATIONS (if needed)
Nov 23 HOLIDAY – no class
Nov 27 Discussion: Network statistics Baranzini Video-Networks1
Video-Networks2
Slides-Graph Theory
Slides-Biological Networks
Nov 28 Coding: Cytoscape Baranzini Install and test Cytoscape
Install and test packages
Nov 29 Paper: Metabolic networks Baranzini/TAs Prepare for paper discussion
Nov 30 Lab: Network analysis Baranzini/TAs Download lab files
Dec 4 Board: Dimension reduction, PCA, t-SNE Ntranos Video-Distances
Slides-Distances
Video-Dimension Reduction
Slides-Dimension Reduction
Slides-PCA
Dec 5 Coding: Visualizing single-cell clusters Ntranos Video-Clustering
Slides-Clustering
R Code
Python Notebook
Dec 6 Paper: Performing dimension reduction Ntranos/TAs Prepare for paper discussion
Dec 7 Lab: Single-cell genomics Ntranos/TAs Download lab files
Dec 11 NO CLASS
Dec 12 PRESENTATIONS
Dec 13 PRESENTATIONS
Dec 14 PRESENTATIONS