Skip to contents
OncoPath 0.0.32 (2025-10-09)
Documentation Improvements
README.Rmd
-
NEW: Created comprehensive README.Rmd with detailed module description
- Enhanced feature descriptions with emojis for better readability
- Added detailed installation instructions (3 methods)
- Included quick start examples for both swimmer and waterfall plots
- Added comprehensive use cases section (Clinical Research, Pathology Research, Publication Support)
- Expanded acknowledgements section with gratitude to package developers
- Integrated with ClinicoPath ecosystem documentation
Documentation Website
- All documentation now available at: https://www.serdarbalci.com/OncoPath/
- Direct links to swimmer plot and waterfall plot guides
- Clear integration with main ClinicoPath documentation hub
Vignette Additions
-
NEW: Added 9 comprehensive vignettes for enhanced documentation
-
Clinical Heatmap:
clinicalheatmap_comprehensive.Rmd - Clinical heatmap visualization
-
Digital Pathology Suite (4 files):
-
digital_pathology_chatgpt.md - AI-generated pathology analysis guide
-
digital_pathology_claude.md - Comprehensive digital pathology documentation
-
digital_pathology_gemini.md - Alternative AI perspective on digital pathology
-
digital-pathology-analysis-suite.md - Complete digital pathology analysis overview
-
Texture Analysis:
HARALICK_TESTING_GUIDE.md - Haralick texture feature analysis testing
-
Agreement Analysis (3 files):
-
COMBINED_USUBUTUN_GUIDE.md - Combined Usubutun plot guide
-
USUBUTUN_ENHANCED_TEST_GUIDE.md - Enhanced testing procedures
-
USUBUTUN_TEST_GUIDE.md - Standard testing guide for agreement visualization
-
Oncoplot:
ggoncoplot_documentation.md - Genomic alteration visualization documentation
Function Documentation
- Added waterfall plot legacy documentation:
09-waterfall-legacy.Rmd
- Function-specific vignette:
06-function-waterfall.Rmd - Detailed waterfall function guide
Features Summary
Patient Follow-Up Plots
- 🏊♂️ Swimmer Plot Analysis: Timeline visualization with ggswim integration
- 🌊 Waterfall Plot Analysis: RECIST criteria treatment response analysis
- Complete support for clinical trial reporting and oncological research
- 🔬 IHC Heterogeneity Analysis: Immunohistochemistry marker analysis
- 📊 Diagnostic Test Meta-Analysis: Bivariate meta-analysis with HSROC
OncoPath 0.0.31.84 (2025-10-03)
Major New Features
-
NEW: Comprehensive diagnostic test accuracy meta-analysis module
- Bivariate random-effects meta-analysis using the Reitsma method
- Hierarchical Summary ROC (HSROC) curve analysis
- Meta-regression capabilities for exploring heterogeneity
- Publication bias assessment with funnel plots
- Support for multiple estimation methods (REML, ML, Fixed Effects, etc.)
- Forest plots for sensitivity and specificity
- SROC plots with confidence regions
- Designed specifically for:
- AI/ML algorithm validation in pathology
- Biomarker diagnostic accuracy synthesis
- Systematic reviews of diagnostic tests
IHC Heterogeneity Analysis
-
NEW: Statistical analysis of immunohistochemistry marker heterogeneity
- Multi-marker evaluation capabilities
- Robust statistical methods for heterogeneity assessment
- Specialized tools for pathology biomarker research
Enhancements
Treatment Response Analysis (Waterfall Plot)
- Improved RECIST criteria implementation
- Enhanced visualization options
- Better handling of longitudinal data
Swimmer Plot
- Continued integration improvements with ggswim package
- Enhanced data validation
- Better error handling and user feedback
Dependencies
New Package Dependencies
-
mada: Meta-analysis of diagnostic accuracy studies
-
metafor: Advanced meta-analysis and meta-regression
-
pROC: ROC curve analysis
-
survival & survminer: Survival analysis support
-
boot: Bootstrap methods
-
dcurves: Decision curve analysis
-
Hmisc: Statistical utilities
-
rms: Regression modeling strategies
-
timeROC: Time-dependent ROC curves
-
tidyr: Data tidying operations
Bug Fixes
- Fixed menu organization for diagnostic meta-analysis
- Improved variable name handling with special characters
- Enhanced error messages and user guidance
Internal Changes
- Updated NAMESPACE with new imports
- Reorganized menu structure for better discoverability
- Added comprehensive validation for meta-analysis inputs
- Improved handling of zero cells in diagnostic data
OncoPath 0.0.31.69 (Previous Version)
Features
- Swimmer Plot Analysis with ggswim integration
- Waterfall Plot Analysis with RECIST criteria
- Treatment Response Visualization
- Patient Timeline Tracking
Initial Release Features
- Comprehensive patient follow-up visualization tools
- RECIST criteria analysis
- Clinical event tracking
- Publication-ready visualizations