ProleTRact v1.1.0

Overview

ProleTRact v1.1.0 adds a file browser, advanced filtering, and workflow improvements. No breaking changes; full backward compatibility with TandemTwister VCF outputs.

Changes

• File browser — Browse button to select VCF files and folders via a file picker instead of entering the full path
• Advanced filtering — Filter by motif size, copy number, chromosomes, genotypes, pathogenic-only; save/load presets
• Mode cache — Switching between Individual and Cohort modes preserves paths, filters, and navigation state
• Region jump — Jump directly to region N from the navigation bar
• Resizable sidebar — Adjustable width with saved preference
• Pathogenicity — Gene search and improved panel layout
• Documentation — bioRxiv citation and updated installation instructions (proletract --install-deps)

ProleTRact_v1.0.1

ProleTRact React-Based Frontend

Overview

ProleTRact v1.0.1: transitions from a Streamlit-based interface to a modern React application. This change addresses scalability limitations and provides a foundation for future development while maintaining all existing functionality.

Technical Changes

Frontend Architecture

• Complete migration from Streamlit to React 18 with TypeScript
• Client-side rendering for improved performance and responsiveness
• Component-based architecture for better code organization and maintainability

The migration from Streamlit to React was driven by several technical and practical considerations:

Performance

React runs in the browser and does not require server round-trips for user actions. This makes the interface faster. Users will notice this when viewing TR regions, filtering data, or doing multiple tasks. The single-page design reduces delays and improves responsiveness.

Flexibility and Customization

React gives full control over how components look and work. This allows building custom visualizations for tandem repeat analysis. Streamlit has limited components.

Scalability

The component-based design makes the code easier to maintain. Adding new features is simpler.

Backward Compatibility

While the frontend has been completely rebuilt, backward compatibility with TandemTwister has been maintained. The main command-line interface remains unchanged.

ProleTRact_v0.2.0

Add Genotype Filtering Feature

This change adds genotype filtering functionality to ProleTRact, allowing users to filter tandem repeat regions by genotype in both individual and cohort modes.

Features

• Genotype Extraction: Extracts genotype information (GT field) from VCF records during parsing
• Filter UI: Added sidebar filter in both Individual and Cohort modes to select genotypes to display

User Experience

• Users can now filter regions by genotype using a multi-select dropdown in the sidebar
• Filtering works seamlessly with existing search and navigation functionality
• Visual feedback shows how many regions match the selected genotypes

ProleTRact_v0.1.1

• Versatile TR exploration. Dedicated pages for individual samples, read-based cohorts, and assembly cohorts.
• Interactive visual analytics. Color-coded motif panels, genotype summaries, population overlays, and cohort clustering.
• Context-aware insights. Built‑in pathogenic catalog, quick links to UCSC/gnomAD/TRExplorer, and other databases.