TeachingDemos

Bioinformatics related demos and tutorials using the R programming language.

Software

• MetaMapR
• DeviumWeb

Installation

www.createdatasol.com

Live examples

R Code Examples and More

Data Analysis Examples

• Metabolomic and Proteomic Data Analysis 2015

Data Wrangling

• dplyr tutorial: verbs and split-apply

Statistical Analysis

• Covariate Adjustment

Principal Components Analysis (PCA)

• pca and scores visualization on custom data (fast and simple)
• pca on mtcars (fast and simple)

PLS

• Partial Least Squares (PLS) (fast and simple)

Predictive Modeling

• O-PLS Example (04/08/15)
• O-PLS-DA compared to Random Forest (updated 11/7/15)
• Comparing single to multiple Y models

Database query and translation

• Translating Between Chemical Identifiers (intermediate)
• CTSgetR

Network Visualizations

• Building Biochemical and Chemical Similarity Networks (advanced)
• [KEGG Pathway Visualization] (https://github.com/dgrapov/TeachingDemos/blob/master/Demos/Pathway%20Analysis/KEGG%20Pathway%20Enrichment.md) (genes, proteins and metabolites)

Miscellaneous

• [Summer 2014 Metabolomic Data Analysis Workshop] (http://imdevsoftware.wordpress.com/2013/09/08/sessions-in-metabolomics-2013/)
• Winter 2014 Metabolomic Data Analysis Workshop
• Data analysis and visualization blog