/Global-analyses-of-the-human-structural-proteome-to-identify-a-new-type-of-disease-biomarker

Primary LanguageRGNU General Public License v3.0GPL-3.0

Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker

Scripts to reproduce the main analysis of:

Mackmull, MT., Nagel, L., Sesterhenn, F. et al. Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker. Nat Struct Mol Biol (2022). https://doi.org/10.1038/s41594-022-00837-0

Main analysis

StructuralVariabiliyCSF.R: Variability of the healthy human CSF structural proteome

LinearModels.R: Structural proteomic changes in CSF of PD patients

RegularizedRegressionModels.R: CSF structural peptides classify healthy vs PD groups

Requirements

Data requirements

Please download supplementary file 12, all data you need for running the analysis is provided there.

System requirements

The code runs on Linux operating systems (Fedora 25) and has not been tested on other versions.

The code was developed on R-version 4.0.3 including following packages:

devtools 2.4.3
glmnet 4.1-1
lawstat 3.4
multimode 1.5
openxlsx 4.2.5
plyr 1.8.7