Changelog

Source: NEWS.md

TSO500R 0.2.0 “Bubo Scandiacus”

Initial public release - December 2025

Features

📥 Data Import

• Parse MetricsOutput.tsv quality control files
• Process CombinedVariantOutput.tsv variant analysis outputs
• Support for DRAGEN pipeline, LocalApp, and ctDNA workflows
• Extract small variants, CNVs, fusions, and splice variants

🔧 Data Processing

• Automated filtering and processing pipeline
• Filter by variant consequence, depth, germline databases, COSMIC IDs
• Parse P Dot notation for protein information
• Integrate TMB and amplification data

📊 Visualization

• Allele frequency plots (distributions, KDE, histograms)
• OncoPrint data preparation
• QC summary tables
• Consistent plotting themes

💾 Export

• DRAGEN-compatible sample sheets
• RData objects
• Excel workbooks

✅ Quality Control

• DNA and RNA QC metrics extraction
• CNV, TMB, and MSI metrics
• Data validation functions

Documentation

• Comprehensive README and function documentation
• GitHub Pages site: https://boehringer-ingelheim.github.io/TSO500R/
• Example workflows

Installation

# Install from GitHub
pak::pak("Boehringer-Ingelheim/TSO500R")

Getting Help

• Report bugs: https://github.com/Boehringer-Ingelheim/TSO500R/issues
• Contact: @christopher-mohr