This repository contains the analytical pipeline for the MAXOMOD project, which focuses on the multi-omic analysis of axono-synaptic degeneration in the motor neuron disease amyotrophic lateral sclerosis (ALS). The project explores sex differences and molecular subclusters in ALS and investigates the MAPK pathway as a potential therapeutic target.
For a detailed understanding of the scientific background and the findings, refer to our paper published on Nature Communications.
Table of Contents
Getting Started
Prerequisites
Clone the git repository:
git clone https://github.com/imsb-uke/MAXOMOD_Pipeline.git ./maxomod
Enter the cloned directory:
cd maxomod
Data Preparation
Human sequencing data: EGAS00001007318 [due to patient data, access is restricted]
Mouse sequencing data: GSE234246
Proteomics data: PXD043300
Phosphoproteomics data: PXD043297
Organize Data
All data should be organized in datasets using the following structures
datasets/
consortium/
/
01_received_data/
/
cohort/
The pipeline expects fastq.gz
files for the sequencing data, txt
files for the proteomics data and csv
files for the phosphoproteomics data.
Please, use DVC to see, which exact file names are required:
dvc status srna_organize_samples proteomics_organize_samples phosphoproteomics_organize_samples rnaseq_nextflow
Automatic download (optional)
To automatically download the RNAseq & miRNAseq data we provide a download script, which can be executed using the following commands:
dvc unfreeze sra_prefetch sra_fastq_dump sra_organize
dvc repro
Reproducing Results
To reproduce the analysis results, execute the following command:
dvc repro
This command will run the predefined pipelines to process and analyze the data according to the methodology described in the associated publication.
All steps will be executed in a docker container automatically using the docker_wrapper.sh
script. All docker images will be automatically downloaded and are available in the Packages section on GitHub.
Contributing
We welcome contributions to enhance the reproducibility and scope of the analysis.
Collaboration
For questions or collaboration offers, please contact the project's principal investigators via email provided on the MAXOMOD project page: MAXOMOD Contact Information.
Version History
main @ 82f5e3e (earliest) Created 5th Nov 2024 at 14:28 by Fabian Hausmann
Add re-usable methods (#3)
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Created: 5th Nov 2024 at 14:28
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