This repository contains multiple complementary analyses of the Ramsey award ME/CFS cohort, including differential gene expression analysis and phenotypic comparison studies.
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a chronic and debilitating illness affecting millions of individuals worldwide. It is characterized by severe fatigue, pain, flu-like symptoms, and cognitive issues. The cause of ME/CFS is not well understood, but evidence suggests a genetic predisposition and dysregulation of the immune system leading to an overactive immune response.
This repository hosts analyses that explore:
- Differential gene expression patterns in ME/CFS patients
- Phenotypic overlap between ME/CFS and other diseases
- Patient phenotypic similarity and clustering
- Disease enrichment analyses
dge-analysis/- Differential gene expression analysis using Rphenotypic-analysis/- Phenotypic comparison analysisvariant-findings-plot/- Variant findings plotting
For Differential Gene Expression Analysis:
- R (v4.5.1 or later)
- RStudio (v2025.05.1+513 or later)
For Phenotypic Comparison Analysis and Variant Findings plot:
- Anaconda3 or Mamba
Common Requirements:
- Git v2.0+
Installation starts with fetching the Git repo and cloning it:
git clone https://github.com/uab-cgds-worthey/mecfs-cohort-analysis.git
cd mecfs-cohort-analysis/For detailed setup instructions for each analysis, see the README files in their respective directories:
- Differential Gene Expression Analysis: See
dge-analysis/README.mdfor detailed R/renv setup instructions - Phenotypic Comparison Analysis: See the phenotypic comparison documentation for conda/mamba environment setup instructions
- Variant Findings plot: See the variant findings documentation for conda/mamba environment setup instructions
The differential gene expression analysis examines transcriptional changes in a cohort of 23 patients diagnosed with ME/CFS using bulk RNA-seq. The analysis identifies genes that are differentially expressed between affected and unaffected conditions, and explores subgroup-specific patterns.
Located in dge-analysis/.
For detailed documentation including setup, input data, workflow instructions, and results, see
dge-analysis/README.md. The complete analysis described in the publication, generated by
subsetted_condition_analysis.Rmd, is available as an .RData file for
download and can be loaded
directly in R using load("path/to/rdata").
- Results and figures can be found in the
dge-analysis/docs/folder - Viewable online at: https://uab-cgds-worthey.github.io/mecfs-cohort-analysis/
A collection of diseases found in the Ramsey award ME/CFS cohort, phenotypes of ME/CFS and those diseases, and analysis scripts for the comparison and visualization of phenotypes between diseases.
Located in phenotypic-analysis/
For detailed documentation including setup, tools, notebooks, and analysis instructions, see
phenotypic-analysis/README.md.
- Results and figures can be found in
phenotypic-analysis/data/results/ - Carruthers ME/CFS diagnositic creteria as HPO terms is defined in phenotypic-analysis/data/mecfs-phenotypes.tsv
Organized metadata and primary variant findings organized in a variant format expected by the pyoncoprint Python library for generating variant oncoplots. The figure generation process is described in the plotting Jupyter notebook
This project is licensed under the GNU General Public License v3.0.