caravagnalab/ProCESS-examples
Apr 2025 – Mar 2026
5 Months active
Languages Used
BashRShellYAMLbashHTML
Technical Skills
BioinformaticsCancer Evolution ModelingComputational BiologyData AnalysisData VisualizationGenomics
AliceAntonello
PROFILE
Aliceantonello
Alice Antonello developed and enhanced cancer evolution modeling and copy number variation analysis pipelines in the caravagnalab/ProCESS-examples repository. She implemented end-to-end validation frameworks for CNA detection, integrating tools such as ASCAT, CNVkit, and Sequenza, and built cross-caller comparison and visualization scripts using R and shell scripting. Her work included refining simulation environments, automating tissue report generation, and improving data management for scalable batch workflows. Alice also created reproducible figure generation scripts and comprehensive documentation in HTML, supporting publication readiness. The depth of her contributions improved reliability, reproducibility, and interpretability of cancer genomics analyses across multiple research scenarios.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
11Total
Bugs
0
Commits
11
Features
7
Lines of code
21,180
Activity Months5
Your Network
17 peopleShared Repositories
17
Azad HaghighiMember
Alberto CasagrandeMember
azadsadrMember
elena-buscaroliMember
ElenaRivaroliMember
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ElenaRivaroliMember
ElenaRivaroliMember
ElenaRivaroliMember
Work History
March 2026
1 Commits • 1 Features
Mar 1, 2026March 2026 monthly summary for caravagnalab/ProCESS-examples: Delivered SPN07 Supplementary Figures Visualization, introducing an R script to generate supplementary figures for the SPN07 study, focusing on visualizing mutation data and evolutionary dynamics in cancer samples. The visuals include pie charts for sample composition, exposure evolution, and univariate VAF distributions, enabling clearer interpretation of clonal evolution and mutation signatures. This work enhances data storytelling, reproducibility, and readiness for publication.
1 Commits • 1 Features
Mar 1, 2026March 2026 monthly summary for caravagnalab/ProCESS-examples: Delivered SPN07 Supplementary Figures Visualization, introducing an R script to generate supplementary figures for the SPN07 study, focusing on visualizing mutation data and evolutionary dynamics in cancer samples. The visuals include pie charts for sample composition, exposure evolution, and univariate VAF distributions, enabling clearer interpretation of clonal evolution and mutation signatures. This work enhances data storytelling, reproducibility, and readiness for publication.
March 2026
July 2025
2 Commits • 1 Features
Jul 1, 2025Monthly summary for 2025-07 focusing on SPN07 Mutation Simulation Enhancements in caravagnalab/ProCESS-examples. Delivered key feature enhancements to improve genetic mutation simulation accuracy, plus comprehensive documentation and configurable options. No major bugs fixed were documented for this period based on provided data.
July 2025
2 Commits • 1 Features
Jul 1, 2025Monthly summary for 2025-07 focusing on SPN07 Mutation Simulation Enhancements in caravagnalab/ProCESS-examples. Delivered key feature enhancements to improve genetic mutation simulation accuracy, plus comprehensive documentation and configurable options. No major bugs fixed were documented for this period based on provided data.
June 2025
4 Commits • 2 Features
Jun 1, 2025June 2025 monthly summary for caravagnalab/ProCESS-examples highlighting key features delivered, major validation improvements, and the resulting business impact. The month focused on strengthening CNV CNA validation and cross-caller analysis to improve reliability and reporting of CNV events across multiple callers.
4 Commits • 2 Features
Jun 1, 2025June 2025 monthly summary for caravagnalab/ProCESS-examples highlighting key features delivered, major validation improvements, and the resulting business impact. The month focused on strengthening CNV CNA validation and cross-caller analysis to improve reliability and reporting of CNV events across multiple callers.
June 2025
May 2025
1 Commits • 1 Features
May 1, 2025May 2025 performance summary for caravagnalab/ProCESS-examples: Delivered a major feature enhancement to the ProCESS Simulation Environment and introduced an automated tissue reports script. No major bugs were documented this month. The changes enable scalable batch executions, improved data organization, and reproducible analytics, accelerating the path from experiments to insights.
May 2025
1 Commits • 1 Features
May 1, 2025May 2025 performance summary for caravagnalab/ProCESS-examples: Delivered a major feature enhancement to the ProCESS Simulation Environment and introduced an automated tissue reports script. No major bugs were documented this month. The changes enable scalable batch executions, improved data organization, and reproducible analytics, accelerating the path from experiments to insights.
April 2025
3 Commits • 2 Features
Apr 1, 2025April 2025: Focused on delivering end-to-end CNA validation and SPN07 cancer evolution enhancements. Key outcomes include expanded SPN07 simulation setup (CNA validation, increased batch resources, mutation-driven design, multiple-clone modeling, data file additions, and phylogenetic-tree generation) and the development of a CNA call validation framework across ASCAT and rRACES with parsing, comparison, and visualization. These efforts improve cross-pipeline accuracy, reproducibility, and business-value by enabling reliable CNA detection, robust simulation experimentation, and scalable batch workflows. Technologies leveraged include R for multi-clone modeling, scripting for batch jobs, data management, and cross-tool visualization.
3 Commits • 2 Features
Apr 1, 2025April 2025: Focused on delivering end-to-end CNA validation and SPN07 cancer evolution enhancements. Key outcomes include expanded SPN07 simulation setup (CNA validation, increased batch resources, mutation-driven design, multiple-clone modeling, data file additions, and phylogenetic-tree generation) and the development of a CNA call validation framework across ASCAT and rRACES with parsing, comparison, and visualization. These efforts improve cross-pipeline accuracy, reproducibility, and business-value by enabling reliable CNA detection, robust simulation experimentation, and scalable batch workflows. Technologies leveraged include R for multi-clone modeling, scripting for batch jobs, data management, and cross-tool visualization.
April 2025
Activity
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Quality Metrics
Correctness85.6%
Maintainability80.0%
Architecture80.0%
Performance68.2%
AI Usage20.0%
Skills & Technologies
Programming Languages
BashHTMLRShellYAMLbash
Technical Skills
BioinformaticsCancer Evolution ModelingCancer GenomicsComputational BiologyConfiguration ManagementCopy Number Variation AnalysisData AnalysisData VisualizationDocumentationGenomic AnalysisGenomicsHigh-Performance ComputingRR ProgrammingR Scripting
Repositories Contributed To
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