BMI206: Statistical Methods

OVERVIEWSYLLABUSREADING –  LABS – RESOURCESFINAL

Syllabus

All class meetings will be 9:30-10:30am in BH-215 unless otherwise indicated

Date Topic Instructor Materials
Sep 28 Pre-requisite review (BMI)
2-2:30pm, Room: MH-1407
TAs Online course
Sep 30 Pre-requisite review (BMI)
11:30-1:00pm, Room: MH-1407
TAs Online course
Oct 1 Pre-requisite review (BMI)
2-2:30pm, Room: MH-1407
TAs Online course
Oct 14 Exploratory data analysis (BMI) Quigley Read
Ch7: EDA from R for Data Science
EDA: data visualization or torture?
Oct 18 Discussion: Overview, Introductions Pollard Slides-Overview
Slides-Statistics Background
Oct 19 Board work: Linear models Pollard Video-Associations
Slides-Associations
Video-Linear Models
Slides-Linear Models
Oct 20 Coding: Model selection Pollard Video-Model Selection
Slides-Model Selection
Code
Oct 21 Lab: Modeling genetic associations Pollard/TAs Download lab files
Install R
Set up / test Jupyter notebooks
Oct 25 Board work: Categorical data Capra Video-Categorical Data
Slides-Categorical Data
Notes-Study Designs
Notes-Count Distributions
Oct 26 Coding: Resampling methods Capra Video-Resampling Methods
Slides-Resampling Methods
Code
Oct 27 Paper: Gene set enrichment Capra Prepare for paper discussion
Oct 28 Discussion: Projects Pollard/TAs
Nov 1 Board: Multiple hypothesis testing Capra Video-Multiple Testing
Slides-Multiple Testing
Nov 2 Coding: Multiple hypothesis testing Capra Code
Nov 3 Paper: TBD Capra Prepare for paper discussion
Nov 4 Lab: Genomic enrichment tests Capra/TAs Download lab files
Nov 8 Board work: Generalized linear models Pollard Video-GLMs
Slides-GLMs
Nov 9 Coding: Fitting GLMs Pollard Code
Nov 10 Paper: Using statistics in lab research
Optional Lab: Statistical testing tutorial
Pollard/TAs Prepare for paper discussion
Nov 11 HOLIDAY – no class
Nov 15 Discussion: Network statistics Baranzini Video-Networks1
Video-Networks2
Slides-Graph Theory
Slides-Biological Networks
Nov 16 Coding: Cytoscape Baranzini Install and test Cytoscape
Install and test packages
Nov 17 Paper: Metabolic networks Baranzini Prepare for paper discussion
Nov 18 Lab: Network analysis Baranzini/TAs Download lab files
Nov 22 PRESENTATIONS Groups 1-2
Nov 23 PRESENTATIONS Groups 3-4
Nov 24 PRESENTATIONS Groups 5-6
Nov 25 HOLIDAY – no class
Nov 29 Board: Dimension reduction, PCA, t-SNE Ntranos Video-Distances
Slides-Distances
Video-Dimension Reduction
Slides-Dimension Reduction
Nov 30 Coding: Visualizing single-cell clusters Ntranos Video-Clustering
Slides-Clustering
Code
Dec 1 Paper: Performing dimension reduction Ntranos Prepare for paper discussion
Dec 2 Lab: Single-cell genomics Ntranos/TAs Download lab files
Dec 6 PRESENTATIONS
Dec 7 PRESENTATIONS
Dec 2 PRESENTATIONS
Dec 8 PRESENTATIONS
Dec 9 PRESENTATIONS