Code used in project: Metagenome analysis of soil-dwelling bacterial decomposers following long-term warming using a reference genome approach

The following directory contains HTML files outlining the code used to generate the results presented in Seojin Jung’s senior thesis in Biology at Amherst College, “Metagenome analysis of soil-dwelling bacterial decomposers following long-term warming using a reference genome approach.” The main repository is here.

HTML files

• Setting up in RStudio
• Generating Sankey plot
• MetaBAT analyses
• Extract traits and build matrices
• Trait selection and processing
• Problematic classification of decomposers
• Hierarchical clustering and heatmap
• Differential abundance analysis

Miscellaneous code not included in main work

• Counts of MAGs per trait
• Initial guild clustering