hichub 0.0.2

Comprehensive Network Analysis for HiC

NOTE: This software is under development.

ON Jan/11/2021, only a demo is included.

Comprehensive Network Analysis for HiC

• Overview
• Documentation
• System Requirements
• Installation Guide
• Example of Running (Demo)
• License

Overview

xxx is a Python package containing tools for network analysis of HiC data. From HiC Interactions, clustering and ranking interaction change among all clustering.

Documentation

The official documentation with usage is under development.

System Requirements

Hardware Requirements

This package requires only a standard computer with enough RAM to support the in-memory operations.

Software Requirements

xxx mainly depends on the Python scientific stack.

python 3
optparse
pandas
numpy
pybedtools
igraph
scipy

Installation Guide

Recommend to use bioconda for installing.

https://bioconda.github.io/user/install.html

Or

pip install numpy optparse pandas pybedtools igraph scipy

Example of Running (Demo)

Input Format: HiC Interaction in txt format. Example of test data can be found in ~/test_data

#chr	bin1	bin2	Cond1	Cond2
10	3000000	3010000	100	200

EXAMPLE:

python igraph_hub.py -i chr10_WT_na-DKO_na.bed -f WT_na -b DKO_na -r 10000 -d 0.5

Options:

  -h, --help            show this help message and exit
  -i <file>, --in=<file> Path to Input HiC file in txt format
  -f <str>, --foreground_name=<str> Name of condition as foreground.
  -b <str>, --background_name=<str> Name of condition as background.
  -r <int>, --resolution=<int>      Resolution of HiC txt
  -d <float>, --filtered_density=<float> Density cutoff for hub shriking.

Output of Hubs:

0	1	2	hub_name	Num_vertices	pvalue
chr10	20930000	21060000	chr10:20930000-21060000	11	7.88966007260005e-09
chr10	19590000	19720000	chr10:19590000-19720000	11	7.809766623341443e-05
chr10	80210000	80340000	chr10:80210000-80340000	11	9.520611432439225e-05
chr10	95890000	96030000	chr10:95890000-96030000	14	0.00015075762147303865

Built With

Contributing

Please read xx.md for details on our code of conduct, and the process for submitting pull requests to us.

Versioning

Authors

• *Xiang Li Initial work

License

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

Acknowledgments

• Hat tip to anyone who's code was used
• Inspiration