Data Analysis of proteomics data for "Zika virus-induced remodeling of ER membranes" project

DOI

A collection of R and Julia scripts for the analysis of data for "SARS-CoV-2/SARS-CoV" project:

• prepare_data.R: MaxQuant data import, normalization, MSGLM model setup
• protregroup.jl: inference of protein groups
• effect_scales_normalize.stan: inference of the scales of AP- and ZikV-associates MSGLM model effects for individual replicates
• msglm_fit_chunk.R: per protein group MSGLM model fitting (run on the LRZ SLURM compute cluster)
• assemble_fits.R: assembling the results of MSGLM model fitting and report generation
• msglm_plots.R: volcano and scatter plots for MSGLM model fitting results