caravagnalab/ProCESS-examples
Jul 2025 – Feb 2026
4 Months active
Languages Used
RShellBash
Technical Skills
BioinformaticsData AnalysisR ProgrammingData WranglingScriptingHigh-Performance Computing
elena-buscaroli
PROFILE
Elena-buscaroli
Worked on the caravagnalab/ProCESS-examples repository, delivering a series of refactors and feature enhancements to streamline subclonal deconvolution analysis workflows. Focused on improving data processing, modularity, and reproducibility, the developer reorganized R and Bash scripts, introduced SLURM batch job orchestration, and enhanced mutation data handling for more robust downstream analysis. They implemented automated reporting and mutation-rate management, consolidating utilities to reduce duplication and support scalable development. By addressing workflow reliability and ensuring data integrity, especially in mutation-rate table generation, the work strengthened the pipeline’s maintainability and reproducibility, leveraging skills in bioinformatics, R programming, data analysis, and high-performance computing.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
5Total
Bugs
0
Commits
5
Features
4
Lines of code
1,182
Activity Months4
Your Network
17 peopleShared Repositories
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Azad HaghighiMember
Alberto CasagrandeMember
AliceAntonelloMember
azadsadrMember
ElenaRivaroliMember
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ElenaRivaroliMember
Work History
February 2026
2 Commits • 1 Features
Feb 1, 2026February 2026 monthly summary for caravagnalab/ProCESS-examples focusing on feature delivery and reliability improvements in the subclonal deconvolution workflow. Key features delivered: - Mutation Rate Analysis Enhancements for Subclonal Deconvolution (Mobster/Process): adds functionality to compute and manage mutation rates for subclonal analyses with enhanced generation of mutation-rate tables. Commits involved include 0813111ad6561c9aedb52f4d5e47a06b447cd28c and eb6ad7d6b1bd2ad4690af456004dc0f512a71cc5. Major bugs fixed: - Ensured unique mutation rate values across generated mutation-rate data to prevent downstream errors, addressing a critical robustness issue. Overall impact and accomplishments: - Strengthened the reliability and reproducibility of Mobster/Process-based subclonal deconvolution analyses within ProCESS-examples. - Improved data integrity and downstream reporting through robust mutation-rate table generation and value uniqueness. Technologies/skills demonstrated: - Mobster and Process integration, mutation-rate management, advanced data-table generation, debugging and robust bug-fix discipline, version-controlled development within a Jupyter/Python data-science workflow.
2 Commits • 1 Features
Feb 1, 2026February 2026 monthly summary for caravagnalab/ProCESS-examples focusing on feature delivery and reliability improvements in the subclonal deconvolution workflow. Key features delivered: - Mutation Rate Analysis Enhancements for Subclonal Deconvolution (Mobster/Process): adds functionality to compute and manage mutation rates for subclonal analyses with enhanced generation of mutation-rate tables. Commits involved include 0813111ad6561c9aedb52f4d5e47a06b447cd28c and eb6ad7d6b1bd2ad4690af456004dc0f512a71cc5. Major bugs fixed: - Ensured unique mutation rate values across generated mutation-rate data to prevent downstream errors, addressing a critical robustness issue. Overall impact and accomplishments: - Strengthened the reliability and reproducibility of Mobster/Process-based subclonal deconvolution analyses within ProCESS-examples. - Improved data integrity and downstream reporting through robust mutation-rate table generation and value uniqueness. Technologies/skills demonstrated: - Mobster and Process integration, mutation-rate management, advanced data-table generation, debugging and robust bug-fix discipline, version-controlled development within a Jupyter/Python data-science workflow.
February 2026
October 2025
1 Commits • 1 Features
Oct 1, 2025Month 2025-10 — Key feature delivered: Subclonal Deconvolution Workflow Enhancements in caravagnalab/ProCESS-examples. Refactored R scripts to add directory existence checks and improved table-joining logic; introduced SLURM batch scripts to streamline job submission for generating and processing subclonal analysis tables. Commit 0f748422d59fc4714db2b379ba48d30a1dc529f5 ("minor changes to subclonal scripts"). No explicit major bug fixes recorded this month; minor adjustments were included within the feature work. Impact: Increased reliability and scalability of subclonal analyses, enabling faster, more reproducible results with reduced manual intervention. Business value: accelerates analysis turnaround, lowers risk of workflow failures, and improves batch processing efficiency. Technologies/skills demonstrated: R scripting, SLURM batch scripting, workflow refactoring, data-table joins, batch job orchestration.
October 2025
1 Commits • 1 Features
Oct 1, 2025Month 2025-10 — Key feature delivered: Subclonal Deconvolution Workflow Enhancements in caravagnalab/ProCESS-examples. Refactored R scripts to add directory existence checks and improved table-joining logic; introduced SLURM batch scripts to streamline job submission for generating and processing subclonal analysis tables. Commit 0f748422d59fc4714db2b379ba48d30a1dc529f5 ("minor changes to subclonal scripts"). No explicit major bug fixes recorded this month; minor adjustments were included within the feature work. Impact: Increased reliability and scalability of subclonal analyses, enabling faster, more reproducible results with reduced manual intervention. Business value: accelerates analysis turnaround, lowers risk of workflow failures, and improves batch processing efficiency. Technologies/skills demonstrated: R scripting, SLURM batch scripting, workflow refactoring, data-table joins, batch job orchestration.
September 2025
1 Commits • 1 Features
Sep 1, 2025Month: 2025-09 — Delivered major refactor and reporting enhancements for the Subclonal Deconvolution Analysis Toolkit in caravagnalab/ProCESS-examples. Focused on modularity, reporting, and automation to support reproducible subclonal analyses across projects.
1 Commits • 1 Features
Sep 1, 2025Month: 2025-09 — Delivered major refactor and reporting enhancements for the Subclonal Deconvolution Analysis Toolkit in caravagnalab/ProCESS-examples. Focused on modularity, reporting, and automation to support reproducible subclonal analyses across projects.
September 2025
July 2025
1 Commits • 1 Features
Jul 1, 2025July 2025 monthly summary for caravagnalab/ProCESS-examples: Delivered a Subclonal Deconvolution Analysis Pipeline Refactor that reorganizes data processing, upgrades mutation data fetching, and streamlines the integration and merging of PyClone and ProCESS results to produce a unified analysis output. The refactor emphasizes maintainability, reproducibility, and clearer data provenance across the subclonal inference workflow.
July 2025
1 Commits • 1 Features
Jul 1, 2025July 2025 monthly summary for caravagnalab/ProCESS-examples: Delivered a Subclonal Deconvolution Analysis Pipeline Refactor that reorganizes data processing, upgrades mutation data fetching, and streamlines the integration and merging of PyClone and ProCESS results to produce a unified analysis output. The refactor emphasizes maintainability, reproducibility, and clearer data provenance across the subclonal inference workflow.
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Quality Metrics
Correctness84.0%
Maintainability84.0%
Architecture80.0%
Performance68.0%
AI Usage20.0%
Skills & Technologies
Programming Languages
BashRShell
Technical Skills
BioinformaticsData AnalysisData WranglingHigh-Performance ComputingR ProgrammingR programmingScriptingbioinformaticsdata analysisstatistical modeling
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