NucleosomeProteomeAnalysis

This was tested using R version 4.2.2

To install dependencies,

run installation.R in RStudio

Step 1: run preproccess.R with

RScript preprocess.R [experiments options: grouping_all | v1 | walk | ap] [/path/to/output/dir]

Step 2: run analysis script for profile plot outputs, PCA, and other protein summarization analysis

Run analysis.Rfor multiple mixture experiment

RScript analysis.R [/path/to/output/dir/with/preprocess/outputs]

Run analysis_single_run.Rfor single-run experiment

RScript analysis_single_run.R [/path/to/output/dir/with/preprocess/outputs]

Step 3: Pairwise analysis

Run change.R to output volcano plots for any experiment

RScript change.R [experiments options: grouping_all | v1 | walk | ap] [/path/to/output/dir/with/preprocess/outputs]

Step 4: Heatmap analysis

Run heatmap.R to output heatmap plots for any experiment

RScript heatmap.R [experiments options: grouping_all | v1 | walk | ap] [/path/to/output/dir/with/preprocess/outputs]