BMI206: Statistical Methods

OVERVIEWSYLLABUSREADING –  LABS – TUTORIALSPROJECT

Syllabus

All class meetings will be 9:30-10:30am in MH-2103 unless otherwise indicated

Date Topic Instructor Materials
TBD Pre-requisite review (BMI)
Time, Location
TAs Online course
MBoC Tutorial
Slides-Statistics Background
TBD Pre-requisite review (BMI)
Time, Location
TAs Online course
MBoC Tutorial
Slides-Statistics Background
TBD Pre-requisite review (BMI)
Time, Location
TAs Online course
MBoC Tutorial
Slides-Statistics Background
TBD Pre-requisite review (BMI)
Time, Location
TAs Online course
MBoC Tutorial
Slides-Statistics Background
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: TBD 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 Coding: Resampling methods Capra Video-Resampling Methods
Slides-Resampling Methods
Code
Oct 19 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?
Download lab files
Nov 7 QBC Retreat: No class
Nov 8 QBC Retreat: No class
Nov 9 QBC Retreat: No class
Nov 10 Lab: Exploratory Data Analysis Quigley/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
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