I have included materials below for lessons I have made for coursework or other avenues of learning.  

Table of Contents:

Computational Genomics Methods

Topics covered:                           (Link to full course materials here)

1. Extracting trends/structure from the data: Clustering

a. Linkage types

b. Distance metrics

c.  Hierarchical clustering

d. K-means clustering

e. Model-based clustering

f.       Network analysis

2. Dimensionality reduction and finding hidden factors: PCA/ICA

a. Principles of dimensionality reduction (finding variance contributions/patterns)

b. Principle Component Analysis (PCA)

c.  Independent Component Analysis (ICA)

d.     t-Distributed Stochastic Neighbor Embedding (tSNE)

3. Enrichment Analysis

a. Hypergeometric/Binomial distributions (statistics of trial successes)

·        Pulling white marbles out of a jar example

b. How this is used in general in Gene Set Enrichment

c.  Gene Ontology analysis / KEGG

d. Tools

·        Amigo

·        Enrichr

4. Different Gene Expression Analysis

a. Brief introduction to upstream data processing

b. Read-counting with aligner (STAR) or pseudoalignment (Salmon)

·        Extra options to model experimental/measurement biases

c.  Importing into R

d. DESeq2 intro

e. Building experimental model table and simple DGE lists (differential gene expression)

f.   Working with interaction terms and more complicated DGE setups

·        LTR vs Wald approaches to DGE

g.     Displaying DEGs (differentially expressed genes)

5. ChIP-seq & ATAC-seq

a. Model-based peak calling (MACS2)

b. Window-based “peak”/read pile-up calling (csaw)

c.  Methods of displaying peak regions

·        IGV

·        GViz package in R

6. Motif Discovery

a. Regular expressions

b. Position Weight Matrices and MEME

c.  SELEX-seq

d.     SMiLE-seq

Weeks 4-8: Differential Gene Expression

Differential Gene Expression (DGE) Analysis                               DGE Analysis Lab                                                     DGE Supplemental/Extra

Weeks 14-15: Working with sequences