Code repository for reproducing analyses in Khoury et al., 2026, PDF, Website
This codebase covers all raw data processing, outputs, analysis, and figure generation.
Raw sequencing and LC-MS/MS data will be made available.
All meta data, processed data, and files required for reproducing all analyses in this repository are accessible via Zenodo DOI: 10.5281/zenodo.22649483
When executing any script or markdown file, always run Install_and_load_packages.R and Functions_for_mapping_and_analysis.R first. To reproduce the exact analysis, run:
- Install_and_load_packages.R
- Functions_for_mapping_and_analysis.R
- n6p2_preprocessing_and_QC.R
- n6p1_preprocessing_and_QC.R
- n3p1_preprocessing_and_QC.R
- n2p2_preprocessing_and_QC.R
- n2p1_preprocessing_and_QC.R
- Protein_data_integration_annotation.R
- SS3xpress_preprocessing_and_QC.R
- PBMC_Covariation.Rmd (scripts 1 through 8)
Meta data, raw data, processed abundance matrices, and .rds files are loaded in each script where needed.
Script 4 in PBMC_Covariation.Rmd is the only script within the markdown file that needs each protein preprocessing script run first, but otherwise can be skipped to proceed with scripts 5-8.
Executing scripts sequentially in PBMC_Covariation.Rmd (main analysis) requires first running:
- Protein_data_integration_annotation.R
- SS3xpress_preprocessing_and_QC.R