Introduction to Pathway Analysis Using R

Description

An introduction to Pathway Analysis using R. We will begin with a tour of common software tools and methods for functional enrichment analysis, including WikiPathways, Cytoscape, RStudio, and the R packages: clusterProfiler, rWikiPathways and RCy3. The hands-on portion will walk through a basic enrichment analysis, including basic data visualization and exploration. We will also cover advanced topics on pathway visualization and publishing figures. We will reserve time to work with your own data and project topics.

Learning Path

   This is an intermediate workshop in the Pathway Analysis series. Prior experience with R is required. See introductory and intermediate R workshops:

• Introduction to R for data analysis
• Intermediate R for data visualization

Materials

• Online slides (downloadable PDF)
• Pathway Analysis Vignette (downloable Rmd)

Pre-workshop Instructions

• Install the basics
• Install additional packages and apps

Online Learning

You can access these materials remotely at any time and go through them at your own pace. Here's how:

1. Perform the pre-workshop instruction steps above.
2. Access the online slides.
3. Go through the slides at your own pace.
4. Hands-on exercise is recommended at the end of the presentation. Here is the notebook (and downloable Rmd).
5. Contact [email protected] with any questions you have and we will reply promptly. For Cytoscape-specific questions, you can access a larger community of help here.