# crosslinking-paper

**Repository Path**: matrix_evolution/crosslinking-paper

## Basic Information

- **Project Name**: crosslinking-paper
- **Description**: The code for paper "rosslinking Intensity Modulates the Reliability and Sensitivity of Chromatin Conformation Detection at Different Structural Levels" finished at Feb. 2024
- **Primary Language**: Python
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2024-02-08
- **Last Updated**: 2024-08-21

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# crosslinking-paper

#### Description
The code for paper "rosslinking Intensity Modulates the Reliability and Sensitivity of Chromatin Conformation Detection at Different Structural Levels" finished at Feb. 2024

#### Architecture
* notebooks: The jupyter notebooks generating the figures (including those as supplementary materials).
* helper_script: A python package for processing the data and generating the figures. The main code for figure generation was in plot_func.py file and encapsulation as classes plotFig1, PlotFig2, etc. 
* source data for graphs.7z: The archived data for generating figures in the paper, including:
    * contact_frequency_decay_curves.xlsx: Data (raw read counts) for plotting the contact frequency curves. 
    * reproducibility score.xlsx: The chromosome-wise reproducibility scores (GenomeDISCO scores and essential distances) between every pair of comparisons. Scores were reported at 50 kbp resolution. 
    * compartment_PC1.xlsx: The (unnormalized) PC1 profiles for compartment assignments. bins with positive values would be assigned as compartment A and those with negative values as B. 
    * insulation_profile_(GM12878/K562).csv: The insulation score profiles. Those bins in incalculable regions were omitted. 
    * called_TADs.xlsx: The called TADs in each cell type and condition. The "start" and "end" are the mid-positions of the upstream and downstream boundaries. 
    * called_loops.xlsx: The called loops in each cell type and condition. The "start" and "end" are the mid-positions of the upstream and downstream loop anchors. The "fdr" and "scale" columns are directly extracted from the output of mustache.