This repository contains all scripts used to analyze the AllerScan sequencing data described in Monaco et al. Profiling Serum Antibodies with a Pan Allergen Phage Library Identifies Key Wheat Allergy Epitopes. All scripts are coded in R 3.6.1 in OSX. To run all enclosed scripts the following libraries are required: RColorBrewer, tidyverse, fpc, data.table, knitr, rafalib, dplyr, gplots, pheatmap,viridis, ggpubr, tidyverse, magrittr, cluster, cowplot, NbClust, clValid, ggfortify, clustree, dendextend, factoextra, FactoMineR, corrplot, GGally, ggiraphExtra, knitr, kableExtra, igraph, vipor, ggbeeswarm, plotly.
Installation of all library packages can take between 15 minutes to an hour to complete. All custom code does not require an installation and can be immediately run in native R after acquistion of the AllerScan data set.
All custom code specifically processes the AllerScan sequence data described in Monaco et al. Profiling Serum Antibodies with a Pan Allergen Phage Library Identifies Key Wheat Allergy Epitopes. Each script is designed to reproduce on the figures present in the manuscript and take between 1 - 5 minutes to run. Each scrit should exactly reproduce a plot in aforementioned manuscript.
All custom code enclosed requires the processed AllerScan sequencing data (which has been compressed into an Rdata object. Upon acquistion of the sequencing data (contact hlarman1@jhmi.edu for access), all scripts can be run as is locally in R/RStudio. All scripts should return the figures presented in the AllerScan manuscript.