Genomics Analysis Tools

A collection of Python utilities for genomic data analysis, focusing on Hi-C, single-cell, and sequence data processing.

Projects

Hi-C Analysis

• translocation_hic.py: Detect potential chromosomal translocations using cooler format Hi-C data
• domain_caller.py: Call megabase-sized domains from bedGraph files
• juicer_2_tadbit.py: Convert Juicer dense matrices to TADbit format
• matrix.py: Convert TADbit matrices to BUTLRTools format

Single-Cell Analysis

• singlecell_DamID.py: Process scDamID data (Kind et al., 2015) into bedGraph format

Sequence Processing

• basemods_separator.py: Parse PacBio base modifications (m6A, m4C) from GFF files
• bismark_chr_cov.py: Add chromosome prefix to Bismark coverage files

Repository Structure

genomics-tools/
├── projects/
│   ├── hic_analysis/
│   ├── scdamid_analysis/
│   └── sequence_processing/
├── src/
│   ├── formats/
│   ├── analysis/
│   └── utils/
├── tests/
└── docs/

Installation

git clone https://github.com/yourusername/genomics-tools.git
cd genomics-tools

Dependencies

• numpy
• pandas
• cooler
• TADbit
• BUTLRTools

Usage Examples

Hi-C Translocation Detection

python src/analysis/translocation_hic.py input.cool

Convert Juicer Matrix to TADbit

python src/formats/juicer_2_tadbit.py -i input.txt -o output.txt

Process scDamID Data

python src/analysis/singlecell_DamID.py input_data.txt output.bedgraph

Project Documentation

Detailed documentation for each project can be found in their respective directories:

• Hi-C Analysis
• scDamID Analysis
• Sequence Processing

Contributing

Contributions are welcome! Please read our contributing guidelines before submitting pull requests.

License

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

Citation

If you use these tools in your research, please cite.

Contact

• GitHub Issues: For bug reports and feature requests