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Hailey

PROFILE

Hailey

Harrison Hampson engineered and maintained the CHCO-Code repository over 18 months, delivering robust analytics pipelines for single-cell RNA-seq, proteomics, and environmental exposure data. He developed modular workflows in R and Python, integrating tools like Seurat, NEBULA, and Quarto to support reproducible data processing, statistical modeling, and visualization across liver, kidney, and organoid datasets. His work emphasized scalable cloud deployment using AWS Lambda and S3, rigorous data cleaning, and harmonization to ensure data integrity. By automating reporting and standardizing analysis pipelines, Harrison improved research reproducibility, accelerated insight generation, and enabled cross-study integration for translational and clinical research teams.

Overall Statistics

Feature vs Bugs

91%Features

Repository Contributions

466Total
Bugs
23
Commits
466
Features
225
Lines of code
1,524,820
Activity Months18

Your Network

109 people

Shared Repositories

53
Shivani RameshMember
Casey SakamotoMember
ddelcastillofMember
hehampsonMember
hmangalapalliMember
Hailey HampsonMember
Hailey HampsonMember
Hailey HampsonMember
Hailey HampsonMember

Work History

March 2026

9 Commits • 5 Features

Mar 1, 2026

March 2026 monthly summary for childhealthbiostatscore/CHCO-Code. This period focused on delivering robust reporting capabilities, setting up scalable pipelines for transcriptomics analyses, and expanding pathway analyses tooling to support cross-variable insights. Key outcomes include improved reporting reliability, groundwork for large-scale pseudobulk RNA analysis, and a Quarto-enabled PFAS reporting workflow with enhanced outputs and documentation.

February 2026

8 Commits • 4 Features

Feb 1, 2026

February 2026: Delivered end-to-end analytical enhancements across CHCO-Code repositories, expanding liver, organoid, DKA, and microbiome analysis capabilities; improved data quality, reproducibility, and readiness for clinical interpretation; implemented robust data movements and visualization to support faster decision-making and reporting.

January 2026

9 Commits • 2 Features

Jan 1, 2026

January 2026: Delivered key features and fixes to CHCO-Code’s microbiome simulation analysis workflow, delivering measurable business value through improved data quality, reliability, and reporting. Key outcomes include a critical bug fix for scenario 1 filtering, a major reorganization and enhancement of the simulation analysis pipeline with new processing functions and debugging support for Bayesian hierarchical models, and substantial improvements to results formatting, bias evaluation, and plotting. These changes streamline analysis, reduce noise, enable more accurate downstream insights, and lay groundwork for scalable analyses and reproducible reporting. Technologies demonstrated include Python-based pipeline engineering, debugging discipline, Bayesian modeling readiness, data handling practices, and plotting/reporting automation.

December 2025

10 Commits • 2 Features

Dec 1, 2025

December 2025 monthly summary for CHCO-Code: Delivered two end-to-end analytics pipelines addressing environmental exposure and omics data for health risk assessment. PFAS exposure analytics pipeline (PANTHER) provides data processing, statistical modeling, visualization, and predictive capabilities for albuminuria as a kidney health indicator, enabling proactive risk scoring. Liver proteomics data pipeline enhancements improve data loading, cleaning (including longitudinal baseline/follow-up handling), analyte processing, and storage using lambda-based workflows for scalable, automated processing.

November 2025

4 Commits • 3 Features

Nov 1, 2025

Month: 2025-11 — Delivered a trio of end-to-end data processing and analysis improvements in childhealthbiostatscore/CHCO-Code, including a new Simulation Results Processing Pipeline, PFAS Data Analysis Enhancements with data integrity fixes, and scRNA-seq Annotation with New Gene Sets. Implemented robust R-based processing scripts, updated data pathways, and integrated additional gene sets to support richer cell-type annotation. These efforts reduce manual steps, improve consistency across simulations, and enhance the reliability of PFAS and scRNA-seq analyses, enabling faster, more accurate decision-making for downstream studies.

October 2025

22 Commits • 10 Features

Oct 1, 2025

Summary for 2025-10: Delivered substantial data workflow enhancements across CHCO-Code, emphasizing reproducibility, data integration, and project hygiene. Implemented adipose tissue transcriptomics workflow and persisted data to GitHub; added a new liver PET file and refreshed existing data; updated TODAY/Teenlabs proteomics and GSEA analyses; remodeled manuscript figures and cleaned environment and paths (removing deprecated code and updating directory structures); expanded clinical variants analysis and cell-type annotations (TGs added, updated TG cell types, oro states and hep balloon category); integrated IR data updates with new sources (CROC, RH) and refreshed IR variables; standardized cell naming across the project; created a new project scaffold; and fixed directory handling to ensure proper project structure. These efforts improved data traceability, accelerated downstream analyses, and supported faster decision-making for manuscript-ready insights.

September 2025

28 Commits • 14 Features

Sep 1, 2025

September 2025 monthly results for childhealthbiostatscore/CHCO-Code: Focused on stabilizing data integrity, accelerating analysis, and improving maintainability to deliver reliable research outcomes and faster publication-readiness. Delivered robust data handling fixes, corrected analysis logic, completed core results pipeline, and enhanced repository hygiene and deployment readiness. Business value includes improved data trust for grants, reproducible analyses, faster iterations, and scalable workflows for proteomics and IPA analyses.

August 2025

11 Commits • 3 Features

Aug 1, 2025

Monthly summary for 2025-08 for repository childhealthbiostatscore/CHCO-Code focused on delivering end-to-end data analysis enhancements across liver PET workflows, cross-study brain biomarkers, and cell-type labeling improvements. Emphasizes business value through improved insight generation, data quality, and reproducibility.

July 2025

15 Commits • 5 Features

Jul 1, 2025

July 2025 monthly summary for CHCO-Code: Key features delivered across the liver and kidney single-cell RNA-seq workstreams, major maintenance improvements, and strong technical execution that enabled cross-cohort clinical insights and reproducibility. Highlights include: Liver scRNA-seq pipeline enhancements with CellChat integration and improved ALT/AST-related visualizations; Cross-cohort liver data integration with NEBULA/DESeq2 differential expression analyses; Kidney organoid marker lists and differential expression; SKAT tutorial and rare variant analysis documentation; Archive old files and stabilize analysis paths, plus a visualization bug fix (UMAP aspect ratio). These efforts delivered measurable business value by improving biomarker interpretability, data consistency, and reproducibility, and expanding the team's capacity to onboard new datasets.

June 2025

19 Commits • 4 Features

Jun 1, 2025

June 2025 monthly summary for CHCO-Code. Delivered end-to-end organoid RNA-seq analysis pipeline with data loading, pseudobulking, QC, NEBULA differential expression, and rich visualizations (UMAP, volcano plots, pathway analysis). Implemented hepatocyte-focused QC, feature selection, PCA, clustering, and NEBULA-based differential expression with enhanced visualization. Completed cross-dataset liver analysis with differential expression and pathway enrichment via NEBULA and IPA, plus proteomics integration, including harmonized data and robust reporting. Established data storage and I/O infrastructure for liver workflows using S3 (via Cyberduck/reticulate) and prepared a Lambda-based deployment to streamline data processing. Also addressed reliability and reproducibility by updating file paths, preprocessing steps, and library dependencies, improving overall workflow stability. These efforts improve end-to-end scalability, reproducibility, and business value by accelerating insight generation from single-cell analyses and enabling cross-study comparisons.

May 2025

42 Commits • 25 Features

May 1, 2025

May 2025 delivered a set of robust data pipeline enhancements and analytics features for CHCO-Code, driving reliability, data integrity, and business value across research workflows. The work laid groundwork for scalable cloud deployment, richer multi-omics analyses, and clearer data provenance while reducing operational risk in production deployments.

April 2025

70 Commits • 43 Features

Apr 1, 2025

April 2025 CHCO-Code monthly summary focusing on business value and technical achievements across the liver analysis pipeline, performance, and data quality efforts. Key features delivered: - Liver analysis enhancements and simulation scaffolding: hepatocyte and cell-type analyses, liver pathways updates, dot plots, and initial simulation scaffolding (commits include 9c5723f1ea..., 74a8625027..., ec7faee101..., c9a02f9bae..., 72cf54e978...). - GSEA and dotplot enhancements: GSEA code improvements and dotplot refinements for key transcripts (commits eaa8f067318..., 9f93398c517...). - Oro pathways and oroboros analysis: updated pathways, titles, and oroboros analysis improvements (commits 43f9ad92f6..., f20ba525e2..., ef64ca06e8...). - Performance and scalability: newly introduced parallelization on Lambda and loop optimizations to boost throughput (commits a451d3f821..., 8b7193e69d..., e31a330f0e...). - Data quality, reporting, and modeling robustness: organoid QC improvements, descriptive statistics and Table 1 updates, Markdown outputs from scripts, and updates to analysis workflow (commits ddb04d4534..., a01ff48d5d..., 1372cf4116..., 3309c98cbb..., 7c062dd5b31...). Major bugs fixed: - Commented out FC calculation to fix broken behavior (commit 234cf9071a...). - MT filtering code error fix and validation across analyses (commit b28b9e80d0...). - Removed age adjustment in analysis (commit 4d9f1fb1d93...). - Removed obese control filter to correct data filtering behavior (commit 2bd655939ed6...). Overall impact and accomplishments: - Significantly accelerated analytical throughput and enabled scalable liver/genomics workflows, while improving result quality, reproducibility, and reporting efficiency. The updated pipeline supports full gene-set workflows and more robust filtering, increasing confidence for downstream business decisions and stakeholder communications. Technologies/skills demonstrated: - Parallel and multicore computing (Lambda, HPC), advanced statistical modeling (covariance modeling, REML), and high-throughput data processing pipelines. Proficiency with GSEA/MSigDB, Oroboros workflows, organoid QC, and automated Markdown/report generation.

March 2025

32 Commits • 20 Features

Mar 1, 2025

March 2025: Delivered end-to-end QC and preprocessing enhancements for scrnaseq data, modularized visualization, refreshed core utilities, and expanded model checks; fixed UMAP labeling bug and improved documentation and project structure to support maintainability and onboarding. These changes improve data quality, reproducibility, and efficiency across CHCO-Code, enabling faster, more reliable downstream analyses.

February 2025

67 Commits • 33 Features

Feb 1, 2025

February 2025 performance summary for childhealthbiostatscore/CHCO-Code. Focused on delivering core data processing enhancements, expanding analytical modeling capabilities, and improving code quality, reproducibility, and workflow hygiene. Key outcomes include end-to-end kidney data updates, mito filtering improvements, liver/kidney analytical modeling upgrades, data integration and terminology standardization, and strengthened scaffolding for multi-analysis workflows, accelerating downstream decision-making and enabling scalable analyses.

January 2025

49 Commits • 18 Features

Jan 1, 2025

January 2025 monthly summary for CHCO-Code: Delivered substantial improvements across kidney and liver analytics, reinforced data loading and configuration, and tightened release process. Key features delivered include Venn Diagram and Kidney Analysis Enhancements, Alt/AST Protein Associations Analysis, Single-Cell Liver Data Processing, Kidney Single-Cell Analysis Enhancements, and Oat Analysis Pipeline Improvements with visualization. Major bugs fixed include auto stash before merges for clean merges and cleanup of accidentally saved files/plots, contributing to more reliable builds. Overall impact: faster, more reliable data processing and richer, integrative analyses across kidney, liver, and brain datasets, enabling actionable insights for translational studies. Technologies demonstrated: Python data processing, scRNA-seq analysis pipelines, data loading/config management, and disciplined version control.

December 2024

40 Commits • 18 Features

Dec 1, 2024

December 2024 performance highlights for CHCO-Code: Delivered feature-rich analytics and repository improvements that enhance reliability, reproducibility, and speed of downstream analyses. Major work included comprehensive code cleanup and refactor to reduce technical debt; expanded cell-type visualization with heatmaps, UMAPs, and per-cell-type expression; kidney and liver analytics growth with metadata management, ALT/AST integration, and DEG/GSEA support; and automation of Git workflows for safer, repeatable releases. A targeted set of bug fixes and hygiene improvements further streamlined the codebase. These changes increase business value by enabling deeper, faster analyses and more maintainable software foundations.

November 2024

30 Commits • 15 Features

Nov 1, 2024

November 2024 performance summary for childhealthbiostatscore/CHCO-Code. Delivered end-to-end data pipeline improvements, integrated senescence analytics, and enhanced visualization capabilities, while improving code quality and maintaining robust data governance. These efforts unlock reproducible data workflows, faster insight generation, and stronger business value for downstream stakeholders.

October 2024

1 Commits • 1 Features

Oct 1, 2024

Monthly summary for 2024-10 focused on repository hygiene and maintainability for CHCO-Code. Executed targeted cleanup to streamline the codebase by removing legacy assets associated with kidney and liver scRNA analyses. The change reduces clutter, storage usage, and cognitive load for contributors, while preserving current workflows and production integrity.

Activity

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Quality Metrics

Correctness83.6%
Maintainability82.6%
Architecture79.0%
Performance71.8%
AI Usage21.6%

Skills & Technologies

Programming Languages

MarkdownPythonQuartoRR MarkdownRmdSQLShellqmd

Technical Skills

AWS LambdaAWS S3Bayesian StatisticsBayesian analysisBayesian statisticsBioinformaticsBioinformatics ScriptingBiostatisticsCellChatCellChat AnalysisClinical Data AnalysisCloud IntegrationCloud StorageCloud Storage IntegrationCode Organization

Repositories Contributed To

1 repo

Overview of all repositories you've contributed to across your timeline

childhealthbiostatscore/CHCO-Code

Oct 2024 Mar 2026
18 Months active

Languages Used

MarkdownRSQLR MarkdownShellRmdPythonQuarto

Technical Skills

Code RefactoringData CleaningFile ManagementBioinformaticsData AnalysisData Visualization