Usage Guide

This section provides step-by-step instructions to configure, run, and manage your analysis.

Project Configuration

1. Customize Configuration Files

Edit the YAML files in the config/ directory to reflect your study parameters: - config_rnaseq_io.yaml: For processing raw input into analysis-ready format.

Each center should create a center-specific config file using the template:

config/<center_or_study_name>.yaml
# Example:
config/ICB_Gide.yaml

Use config/config_local.yaml as a reference.

2. Add Input Data

Place your raw input datasets (e.g., .rds files) in the data/rawdata/ directory:

data/rawdata/ICB_Gide.rds

Also include gene signature metadata files:

signature.rda
signature_information.csv
Precompiled .RData file — Zenodo DOI: 10.5281/zenodo.18509237

Running Your Analysis

1. Install Dependencies

If using pixi:

pixi install

This sets up your environment with R, Bioconductor, and required packages.

2. Run Local Processing

Prepare analysis-ready .rda files from raw data:

Rscript workflow/scripts/runProcData.R

3. Run Signature Scoring

Rscript workflow/scripts/runSigScore.R

4. Run Association-analysis

Rscript workflow/scripts/runSigAssoc.R

5. Run Meta-analysis

Rscript workflow/scripts/runMeta.R

6. Generate Visualizations

Rscript workflow/scripts/runVisualization.R

This script generates forest plots, volcano plots, and heatmaps. Note: runSigCluster.R and runCorr.r are considered to study signatures' distributions.

Tips for Managing Your Data

Use meaningful filenames (e.g., ICB_Gide__Melanoma__PD-(L)1.rda)