FUS-ALS Molecular ALS Phenotype Scores

This directory contains scripts used to process and analyze screens from the ALS patient-derived fibroblast study. We provide a Dockerfile to install all dependencies for running analyses reported in Kumbier et al. 2024.

  docker build -t als/als .
  docker run -it --rm -v <path to project_als directory>:/ALS als/als

The core analysis scripts used for each screen / analysis include:

General scripts

• preprocessing: directory containing scripts for processing raw image-derived features into the selected set of ALS-relevant eigenfeatures. Proecsses image features are available in the data_profiles directory of the zenodo repository. Raw image features and images are available upon request.

• utilities.R: script containg functions for fitting models along with helper functions for data processing and visualization.

• color_palette.R: sets color palette used in figures.

Analysis specific scripts

Scripts used to generate figures for the paper have been copied to paper_figures and are for the most part organized by figure.

• Figure_Search: analyses of imaging marker set search—reported in supplemental section.

• Figure_Scores: analyses for image-based scores (i-MAP scores).

• Figure_Transcriptomics: analyses for transcriptomic-based scores (t-MAP scores).

• Figure_ASO: analyses from ASO screen. Note: some of the sporadic figures are generated in Figure_Transcriptomics

Data

Data are available through the Zenodo repository: https://zenodo.org/records/10499037. Data for image-based cell profiles are contained in data_profiles, organized by screen. All other data can be found in data.