# Remodelling of enhancer landscape in autoimmune diseases

The scripts used in the analysis with their description are tabulated as follows:

| Description| Folder/Scripts |
| --- | --- |
|  ChIP-seq analysis|ChIP-seq workflow |
|  Functions used in the analysis|functions_used.R
|  Peak Calling| peak_calling_macs2 |
|  Generating Consensus peakset| Psoriasis_SLE_Graves_JIA_making_consensuspeakset.R |
|  Differential Peak analysis| Psoriasis_Graves_SLE_JIASF_consensus_peaks_de.R |
|  K-means clustering of consensus peakset| kmeans_clustering_all_diseases.R |
|  GREAT enrichment analysis | GREAT_analysis_kmeans_cluster_with_JIASF.R |
|  Generating AD GRN| AD_GRN