README.md

Metadomain_Paper

Welcome to the repository for "Metadomain Genome Associations in Mammalian T Cells." This repository contains the code, plots, and data used to generate the figures for the study, which explores the interactions of metadomains within the genome of mammalian T cells.

Overview

This repository is organized to provide easy access to the resources used in generating the main and supplementary figures of the paper, as well as other specific analyses.

Main and Supplementary Figures

• Main Figures: Most of the main figure plots can be found in the Final_Main_Figures.ipynb notebook.
• Supplementary Figures: Most of the supplementary plots are in the Final_Supplementary_Figures.ipynb notebook.

Specific Analyses

• cABC Analysis: Available in the cABC_analysis folder.
• Pileups: Available in the pileups folder.
• ChIP-seq Compendium Analysis: Available in the chip_compendium_analysis folder.
• Hi-C Compendium / Metaloop Analysis: Available in the hic_compendium_analysis folder.

Intermediate Files

• Intermediate files used in the main figure plots, including metadomain calls, loops, etc., can be found in the intermediate_files folder.

Code for Specific Tasks

• Metadomain Calling: Code to call metadomains can be found in the identify_metadomains folder.
• Metaloop Calling: Code to call metaloops can be found in the hic_compendium_analysis/Final_Metaloops_Refine folder.
• Python Scripts: Additional Python code used in the notebooks can be found in the code folder.

Large Files

• Large files, including mcool files and ChIP-seq data, are available on Google Drive: https://drive.google.com/drive/folders/1bsxRWz-5rAUNe-3OctKurxgIj7hCoTOs?usp=sharing

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