Ultimagen/ugbio-utils
Jun 2026 – Jun 2026
1 Month active
Languages Used
Python
Technical Skills
HDF5Jupyter NotebookPythonPython programmingbioinformaticscommand line interface
shay perchik
PROFILE
Shay Perchik
Worked on the Ultimagen/ugbio-utils repository to enhance the SRSNV XGBoost pipeline, focusing on faster VCF preparation and improved evaluation metrics. Introduced a new command line interface for annotation VCF preparation, added flexible filter operators, and refactored k-fold and chromosome splitting logic for more maintainable training workflows. Improved reporting by adding recall metrics at new thresholds and simplifying mixed-reads data presentation while preserving backward compatibility in HDF5 storage. Addressed plot stability for single-fold configurations by implementing a constant standard deviation fallback. Utilized Python, HDF5, and Jupyter Notebook, emphasizing robust data processing, statistical modeling, and unit testing practices.
Overall Statistics
Feature vs Bugs
67%Features
Repository Contributions
4Total
Bugs
1
Commits
4
Features
2
Lines of code
9,357
Activity Months1
Your Network
23 peopleSame Organization
@ultimagen.com10
Shared Repositories
13
Work History
June 2026
4 Commits • 2 Features
Jun 1, 2026June 2026: Delivered major SRSNV/XGBoost pipeline enhancements, reporting improvements, and robustness fixes in Ultimagen/ugbio-utils. Focused on business value: faster VCF preparation, improved evaluation metrics, and a more maintainable codebase across training, reporting, and plotting.
4 Commits • 2 Features
Jun 1, 2026June 2026: Delivered major SRSNV/XGBoost pipeline enhancements, reporting improvements, and robustness fixes in Ultimagen/ugbio-utils. Focused on business value: faster VCF preparation, improved evaluation metrics, and a more maintainable codebase across training, reporting, and plotting.
June 2026
Activity
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Quality Metrics
Correctness90.0%
Maintainability80.0%
Architecture80.0%
Performance80.0%
AI Usage70.0%
Skills & Technologies
Programming Languages
Python
Technical Skills
HDF5Jupyter NotebookPythonPython programmingbioinformaticscommand line interfacedata analysisdata processingdata visualizationmachine learningsoftware developmentstatistical modelingunit testing
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