A collection of portable and reusable data analysis utilities designed for bioinformatics research, with a focus on protein interaction network analysis and transcriptomics integration.
This repository contains modular analysis tools that can be easily integrated into different projects without hard-coded file paths or project-specific dependencies. All tools are designed to be path-agnostic and accept data inputs through parameters.
- python/ - Python utilities and modules
- R/ - R functions and scripts
- utils/ - Cross-platform utilities and configurations
- docs/ - Documentation and integration guides
- README.md - This file
- LICENSE - License information
- Path Agnostic: No hard-coded file paths; all inputs specified via parameters
- Modular: Each tool serves a specific analytical purpose
- Portable: Easy to copy and integrate into different projects
- Well-Documented: Clear function signatures and usage examples
- Language Flexible: Support for both R and Python workflows
- Protein interaction network analysis
- Transcriptomics data integration
- Network topology analysis
- Functional enrichment analysis
- Multi-omics data integration
- Statistical analysis and visualization
For instructions on how to integrate bio-utils into your projects using Git submodules or sparse-checkout, see the integration documentation.
Quick start:
# Add as submodule
git submodule add https://github.com/username/bio-utils.git tools
# Or see docs/quick_reference.md for more optionsWhen adding new tools:
- Ensure no hard-coded paths
- Include comprehensive documentation
- Provide usage examples
- Follow consistent naming conventions
- Test with different input formats
All date outputs use YYYY-MM-DD format consistently across tools.
This project is licensed under the MIT License - see the LICENSE file for details.
Note: This repository focuses on reusable analytical components rather than complete analysis pipelines. For project-specific workflows, create separate repositories that import these tools.