HiChIP Manuscript Code

This repository contains the analysis and plotting scripts for the HiChIP manuscript, designed to process and analyze data from TCGA enhancers and gene interactions.

Table of Contents

• Installation
• Usage
• Code Overview
• Contributing
• License
• Acknowledgements

Installation

Clone the repository:

git clone https://github.com/NCICCGPO/HiChIP-Manuscript.git
cd HiChIP-Manuscript

Install the necessary dependencies for R and Python scripts. You may need R, Python 3.x, and the following libraries:

• R packages: ggplot2, dplyr, etc.
• Python packages: matplotlib, numpy, etc.

For R:

install.packages(c("ggplot2", "dplyr", ...))

For Python:

pip install matplotlib numpy

Usage

The repository contains multiple R and Python scripts, each performing different tasks related to HiChIP analysis. Below are the primary scripts and their usage:

1. TCGA Enhancer Analysis:

   • 1_TCGA_Enhancers_Gene_Interactions.r: Analysis of enhancer-gene interactions using TCGA data.
   • 2_TCGA_Enhancer_Copy_Number_Regression.r: Performs regression analysis on enhancer copy number data.

   Example:

   Rscript 1_TCGA_Enhancers_Gene_Interactions.r

2. RNA Modeling:

   • 3_TCGA_RNA_Modeling.r: RNA modeling analysis for TCGA data.
   • 4_TCGA_RNA_Modeling_Analysis.r: Detailed RNA modeling analysis.

   Example:

   Rscript 3_TCGA_RNA_Modeling.r

3. Visualization:

   • Plot_heatmaps.R: Plots heatmaps for various interaction data.
   • plot_neoloop_dist.py: Python script for plotting neo-loop distributions.

   Example:

   python plot_neoloop_dist.py

For more detailed usage, see each script's comments and documentation.

Code Overview

• Enhancer Analysis:

  • 1_TCGA_Enhancers_Gene_Interactions.r
  • 2_TCGA_Enhancer_Copy_Number_Regression.r
  • TCGA_King_Enhancer_Interaction_Functions.r

• RNA Modeling:

  • 3_TCGA_RNA_Modeling.r
  • 4_TCGA_RNA_Modeling_Analysis.r
  • TCGA_King_RNA_modeling_functions.r

• Visualization:

  • Plot_heatmaps.R
  • plot_neoloop.py
  • Plot_EIS.R

• Workflow Scripts:

  • HiChIP_decomposition_workflow.R: Main workflow for HiChIP data decomposition.
  • Non_coding_workflow_Final.R: Non-coding region workflow.

Contributing

If you'd like to contribute, please fork the repository and use a feature branch. Pull requests are welcome.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgements

This project was developed with data from TCGA and contributions from multiple collaborators in the HiChIP community.