Contents Overview Repo Contents System Requirements Installation Guide Figures Data License Citation Overview This study identifies plasma protein biomarkers for ALS and develops predictive models for phenoconversion. We analyze differentially regulated proteins, describe their longitudinal trajectories, and build models to predict disease onset and timing. Findings are replicated using UK Biobank data. Repo Contents figure/R scripts and generated figures for each main figure panel Fig1–Fig5: Main figure scripts and results Supplement_Figure: Supplementary figure scripts and results data/ analysis_data: processed datasets (not included) fig_data: figure-specific summary data individual_data: patient-level data (not included) summary_data: summary statistics and aggregated results analysis/Additional analysis scripts images/Project schematics and figures System Requirements Hardware Minimum: 4 GB RAM 2 CPU cores Recommended: 16 GB RAM 4 CPU cores @ 3.0+ GHz Supported Operating Systems Linux (Ubuntu 18.04 or newer) macOS (10.14 or newer) Windows 10 or newer R Requirements Tested on: R version 4.4.0 (2024-04-24) or newer Key R packages used include:arrow, cowplot, dplyr, extrafont, ggforce, ggnewscale, ggplot2, ggplotify, ggpubr, ggraph, ggrepel, ggsignif, ggtext, gprofiler2, gridExtra, here, igraph, jtools, kableExtra, knitr, lme4, lmerTest, OlinkAnalyze, patchwork, pheatmap, progress, purrr, RColorBrewer, scales, stringr, tibble, tidygraph, tidyr, tidyverse, UpSetR. A full list is stored in the repository. Installation Guide Install R Ubuntu: sudo apt-get update sudo apt-get install r-base r-base-dev macOS / Windows:Download from CRAN: https://cran.r-project.org/ (copy/paste manually; Zenodo cannot render links) Install R Packages Run in R: install.packages(c('tidyverse', 'OlinkAnalyze', 'lme4', 'lmerTest', 'gprofiler2', 'igraph', 'tidygraph', 'pheatmap', 'ggplot2', 'dplyr', 'gridExtra', 'ggraph', 'RColorBrewer', 'ggpubr', 'cowplot')) Some figures require additional dependencies; see individual scripts. Figures Scripts and results for each figure are located within the figure/ directory. Main Figures Figure 1 – Plasma marker differential regulationDirectory: figure/Fig1 Fig_1A_volcano.png Fig_1B_up_enrichment.png Fig_1C_down_enrichment.png Fig_1D_ppi_network.png Fig_1E_heatmap.png Figure 2 – Longitudinal trajectory of biomarkersDirectory: figure/Fig2 Fig_2A_Temporal_Heatmap.png Fig_2B_Key_Protein_Trajectories.png Figure 3 – Phenoconversion event predictionDirectory: figure/Fig3 Fig_3A_ROC_LR.png Fig_3B_heatmap_single_protein_LR.png Fig_3C_upset_optimal_model_plot.png Figure 4 – Time-to-phenoconversion estimationDirectory: figure/Fig4 Fig_4_combined_tobit_model_prediction_vs_observed.png Figure 5 – UK Biobank replicationDirectory: figure/Fig5 Fig_5A_Replication_vs_discovery_correlation.png Fig_5B_UKB_heatmap_1yr.png Fig_5C_UKB_pre_ALS_2yr_NEFL_EDA2R.png Fig_5D_UKB_DA_model.png Supplementary Figures Located in: figure/Supplement_Figure Sup_Fig1A_All_group_visit_followup_time.pdf Sup_Fig2A_Discovery_ALS_all_81.pdf Sup_Fig2B_Discovery_ALS_convert_pre_post_74.pdf Sup_Fig2C_Discovery_ALS_convert_pre_54.pdf Sup_Fig4_AUC.pdf Data Summary dataStored in: data/fig_data/summary_dataThese files are included and used for figure regeneration. Individual-level dataStored in: data/fig_data/individual_data (excluded from upload) Analysis dataStored in: data/analysis_data (excluded from upload) License See the LICENSE file included in this record. Citation If you use this code or data, please cite: Ran, X., Wuu, J., Qin, Z. S., Cooper-Knock, J., Granit, V., Grignon, A.-L., Li, Y., Lin, E., Fernandez, M. C., Colato, D., Carberry, N., Lill, C. M., Piazza, P., Malaspina, A., & Benatar, M. (2025). Predicting Phenoconversion to Clinically Manifest ALS: Results of a Large-Scale Proteomic Study. Zenodo. https://doi.org/10.5281/zenodo.17852153 Please also cite the associated publication once available.