OSU-BMBL/BMBL-analysis-notebooks
Oct 2024 – Apr 2026
5 Months active
Languages Used
CSSHTMLMarkdownRBashPythonShell
Technical Skills
CSS StylingDocumentationFront-end DevelopmentHTML StructureBioinformaticsData Analysis
Cankun Wang
PROFILE
Cankun Wang
Over five months, contributed to the OSU-BMBL/BMBL-analysis-notebooks repository by developing and documenting end-to-end bioinformatics workflows for single-cell RNA-seq and ATAC-seq analysis. Delivered features such as a digital karyotype pipeline, integrated pathway enrichment using clusterProfiler, and enhanced data visualization with custom UI components. Leveraged Python, R, and shell scripting to implement reproducible pipelines, automate data processing, and coordinate cross-language analyses. Focused on technical writing and prompt engineering to improve onboarding, reproducibility, and collaboration. Emphasized code quality through standardized guidelines and comprehensive documentation, enabling researchers to efficiently interpret complex biological data and streamline multi-omics analysis workflows.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
16Total
Bugs
0
Commits
16
Features
9
Lines of code
621,023
Activity Months5
Your Network
4 peopleShared Repositories
4
Work History
April 2026
1 Commits • 1 Features
Apr 1, 2026Month 2026-04 | OSU-BMBL/BMBL-analysis-notebooks: Delivered enhanced ATAC-seq analysis workflow with integrated pathway enrichment using clusterProfiler, expanding from data processing to functional interpretation. Feature merged via PR and ready for production use. No major bugs reported this period; no fixes required.
1 Commits • 1 Features
Apr 1, 2026Month 2026-04 | OSU-BMBL/BMBL-analysis-notebooks: Delivered enhanced ATAC-seq analysis workflow with integrated pathway enrichment using clusterProfiler, expanding from data processing to functional interpretation. Feature merged via PR and ready for production use. No major bugs reported this period; no fixes required.
April 2026
January 2026
5 Commits • 4 Features
Jan 1, 2026During January 2026, delivered a complete LP-WGS digital karyotype pipeline (including preprocessing scripts, CNV calling, and comprehensive documentation), enhanced Slingshot-based trajectory analysis for scRNA-seq with cell-type proportion analysis and pseudotime dynamics, implemented GEO data retrieval and H5AD conversion workflows to improve data accessibility, and standardized coding guidelines and folder structure to boost consistency and collaboration. No major bugs fixed this month; focus was on feature delivery and code quality improvements. These efforts collectively improve end-to-end data processing, reproducibility, and accessibility, enabling faster, more reliable analyses and clearer project organization.
January 2026
5 Commits • 4 Features
Jan 1, 2026During January 2026, delivered a complete LP-WGS digital karyotype pipeline (including preprocessing scripts, CNV calling, and comprehensive documentation), enhanced Slingshot-based trajectory analysis for scRNA-seq with cell-type proportion analysis and pseudotime dynamics, implemented GEO data retrieval and H5AD conversion workflows to improve data accessibility, and standardized coding guidelines and folder structure to boost consistency and collaboration. No major bugs fixed this month; focus was on feature delivery and code quality improvements. These efforts collectively improve end-to-end data processing, reproducibility, and accessibility, enabling faster, more reliable analyses and clearer project organization.
June 2025
5 Commits • 2 Features
Jun 1, 2025June 2025 Monthly Summary — OSU-BMBL/BMBL-analysis-notebooks Key features delivered: - Enhanced AI-assisted README generation prompts: Created and refined the README-prompt.md to support AI-generated READMEs with a structured analysis prompt and sections (Overview, Getting Started, Usage, Methods, Reproducibility), added environment testing prompts, clarified terminology, and placeholder-based instructions. This work spanned four commits: dbaf6984f271a8371a6cbc2118e84c0f485f0892; 9c19e42e859c2075dfab54d8a0806e0acd19d96a; ce1d19c46fef1051b7fc7aa8986e989597579868; f247923c1468f41fc210647bd6006ab51e69932a. - ArchR/Cicero ATAC-seq tutorials expansion and NOTCH1 iPSC cardiac differentiation scRNA-seq tutorial: Expanded single-cell ATAC-seq tutorials and introduced a comprehensive NOTCH1 iPSC cardiac differentiation scRNA-seq tutorial covering data loading, integration, cell type annotation, differential expression, and trajectory analysis (commit: 7d1652432dac2e716102847228503e1e39df455a). Major bugs fixed: - No explicit bugs reported this month. Focused on documentation and tutorial improvements that enhance reliability, reproducibility, and onboarding. Overall impact and accomplishments: - Significantly improved documentation quality and AI-assisted generation fidelity, enabling faster generation of consistent READMEs and better onboarding for new contributors. - Delivered end-to-end tutorials that lower the barrier to reproducing ArchR/Cicero ATAC-seq analyses and NOTCH1 iPSC cardiac differentiation workflows, improving research reproducibility and knowledge transfer. - Strengthened repository readiness for collaboration and education by providing structured prompts and comprehensive tutorials. Technologies/skills demonstrated: - Prompt engineering for AI-assisted documentation; structured prompt design and environment testing prompts. - ArchR and Cicero ATAC-seq tutorial development; NOTCH1 iPSC cardiac differentiation scRNA-seq workflow (data loading, integration, cell type annotation, differential expression, trajectory analysis). - Bioinformatics data handling within notebooks; git-based collaboration and multi-commit feature delivery; emphasis on reproducibility and onboarding.
5 Commits • 2 Features
Jun 1, 2025June 2025 Monthly Summary — OSU-BMBL/BMBL-analysis-notebooks Key features delivered: - Enhanced AI-assisted README generation prompts: Created and refined the README-prompt.md to support AI-generated READMEs with a structured analysis prompt and sections (Overview, Getting Started, Usage, Methods, Reproducibility), added environment testing prompts, clarified terminology, and placeholder-based instructions. This work spanned four commits: dbaf6984f271a8371a6cbc2118e84c0f485f0892; 9c19e42e859c2075dfab54d8a0806e0acd19d96a; ce1d19c46fef1051b7fc7aa8986e989597579868; f247923c1468f41fc210647bd6006ab51e69932a. - ArchR/Cicero ATAC-seq tutorials expansion and NOTCH1 iPSC cardiac differentiation scRNA-seq tutorial: Expanded single-cell ATAC-seq tutorials and introduced a comprehensive NOTCH1 iPSC cardiac differentiation scRNA-seq tutorial covering data loading, integration, cell type annotation, differential expression, and trajectory analysis (commit: 7d1652432dac2e716102847228503e1e39df455a). Major bugs fixed: - No explicit bugs reported this month. Focused on documentation and tutorial improvements that enhance reliability, reproducibility, and onboarding. Overall impact and accomplishments: - Significantly improved documentation quality and AI-assisted generation fidelity, enabling faster generation of consistent READMEs and better onboarding for new contributors. - Delivered end-to-end tutorials that lower the barrier to reproducing ArchR/Cicero ATAC-seq analyses and NOTCH1 iPSC cardiac differentiation workflows, improving research reproducibility and knowledge transfer. - Strengthened repository readiness for collaboration and education by providing structured prompts and comprehensive tutorials. Technologies/skills demonstrated: - Prompt engineering for AI-assisted documentation; structured prompt design and environment testing prompts. - ArchR and Cicero ATAC-seq tutorial development; NOTCH1 iPSC cardiac differentiation scRNA-seq workflow (data loading, integration, cell type annotation, differential expression, trajectory analysis). - Bioinformatics data handling within notebooks; git-based collaboration and multi-commit feature delivery; emphasis on reproducibility and onboarding.
June 2025
March 2025
3 Commits • 1 Features
Mar 1, 2025March 2025 monthly summary for OSU-BMBL/BMBL-analysis-notebooks. Delivered documentation improvements for the scRNA-seq workflow, enhancing usability, onboarding, and reproducibility. Consolidated and expanded the README to clarify data input formats, general workflow steps, and directory structure. Expanded the methods section with detailed guidance on Cell Ranger processing, Seurat preprocessing, batch removal, cell type annotation, and DEG/pathway analysis; included batch correction guidance and example code using Harmony. Completed documentation updates across multiple commits to improve consistency and future maintainability.
March 2025
3 Commits • 1 Features
Mar 1, 2025March 2025 monthly summary for OSU-BMBL/BMBL-analysis-notebooks. Delivered documentation improvements for the scRNA-seq workflow, enhancing usability, onboarding, and reproducibility. Consolidated and expanded the README to clarify data input formats, general workflow steps, and directory structure. Expanded the methods section with detailed guidance on Cell Ranger processing, Seurat preprocessing, batch removal, cell type annotation, and DEG/pathway analysis; included batch correction guidance and example code using Harmony. Completed documentation updates across multiple commits to improve consistency and future maintainability.
October 2024
2 Commits • 1 Features
Oct 1, 2024Month: 2024-10 — Concise monthly summary focusing on business value and technical achievements for OSU-BMBL/BMBL-analysis-notebooks. This month centered on delivering a new visualization feature, documenting its usage, and reinforcing stable delivery practices.
2 Commits • 1 Features
Oct 1, 2024Month: 2024-10 — Concise monthly summary focusing on business value and technical achievements for OSU-BMBL/BMBL-analysis-notebooks. This month centered on delivering a new visualization feature, documenting its usage, and reinforcing stable delivery practices.
October 2024
Activity
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Quality Metrics
Correctness94.4%
Maintainability90.6%
Architecture89.4%
Performance87.4%
AI Usage37.6%
Skills & Technologies
Programming Languages
BashCSSHTMLMarkdownPythonRShell
Technical Skills
ArchRBioinformaticsBioinformatics DocumentationCSS StylingCiceroData AnalysisData VisualizationDocumentationFront-end DevelopmentHTML StructureHarmonyMonocle3NextflowPrompt EngineeringPython programming
Repositories Contributed To
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