Choose Your Adventure (L24)

Choose Your Own Adventure

Class: Wednesday, April 16th no in-person class

You’ve built a strong foundation in R—now it’s time to put those skills to work! In these quick challenges, you can choose to do 1, 2, or all of them!

Multipanel Figure Creation

Use ggplot2, patchwork, or cowplot to craft a polished, PDF "publication-ready" figure that tells a clear visual story.

Completed tutorial can be found here

Find the data folder here:

/gpfs1/cl/mmg3320/course_materials/R_tutorials/multi_panel_figure

Microbiome Analysis with ampvis2

Dive into microbiome data using ampvis2, a powerful R package designed for simplified analysis and visualization. Easily generate ordination plots, heatmaps, and alpha/diversity metrics.

Completed tutorial can be found here

Find the data folder here:

/gpfs1/cl/mmg3320/course_materials/R_tutorials/microbiome

Gene Set Enrichment Analysis (GSEA)

Continue using clusterProfiler to interpret gene expression results and uncover enriched biological pathways. Rather than just focusing on individual genes, GSEA analyzes gene sets as a whole, making it particularly useful for understanding complex biological processes and disease mechanisms.