Data and Analysis from "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells"

Data, data processing and data analysis for manuscript "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells". Contains the following scripts as well as their outputs: 01_preparation.R R script for filtering and processing our mass spec data. 02_diffbinding.R R script for differential analysis followed by gene set enrichment. 03_funcstats.R R script for statistical analysis over different ontology terms. 04_semantic_analysis.R R script for the GO semantic analysis for the output of 02 and 03. 05_1_random_walks.py Python script for performing random walks for specific functional terms. 05_2_random_walks_analysis.R R script for the analysis and visualization of the output of 05_1. The required input data is deposited in the "data" folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) entry. Interactive visualization of the results of most of this analysis is available on GitHub as a Shiny app.