TeachingDemos

Bioinformatics related demos and tutorials using the R programming language.

#Demos My trial server is up !!!. If you want to test MetaMapR and DeviumWeb you can contact me at dgrapov at gmail.com.

• MetaMapR
• DeviumWeb

#Older Demos (see above for current versions)

• MetaMapR
• Data Visualization
• Heatmaps and Hierarchical Cluster Analysis
• Principal Components Analysis
• Devium

#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

PCA

• Principal Components Analysis (PCA) (fast and simple)

PLS

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

O-PLS/ O-PLS-DA

• O-PLS Example (04/08/15)
• Model permutation testing and validation
• 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