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yzyzero0098/README.md

Jiyeong Lee

Research-oriented GitHub profile for reproducible omics workflows, public analysis notes, and privacy-aware automation templates.

Research Interests

  • Microbiome
  • Metabolomics
  • Transcriptomics
  • Proteomics
  • Shotgun metagenomics
  • Multi-omics integration
  • Bioinformatics
  • Reproducible research automation

Representative Repositories

  • omics-research-kit
    Public workflow kit for microbiome, shotgun metagenomics, transcriptomics, proteomics, and multi-omics reproducibility notes.

  • thermo-glycine-analysis
    Curated analysis workspace for heat-stress glycine supplementation, including 16S microbiome, RNA-seq, phenotype, and integration scripts.

  • loop-engineering-agent-template
    Synthetic agent-loop engineering template with task queues, deterministic tools, evaluator gates, retry states, and audit reports.

  • asset-analysis-loop-template
    Synthetic analysis-loop template with normalization, feature building, scoring, ranking, and review-report generation.

  • asset-report-automation-methods
    Sanitized template for report collection, parsing, normalization, reconciliation, and dry-run validation.

Current Focus

I am organizing local research workflows into public, citable repositories that separate reusable code and documentation from private raw data. The goal is to make research automation easier to inspect, reproduce, and adapt.

Methods And Tools

  • R and Python for omics data analysis
  • QIIME2 and PICRUSt2 for microbiome workflows
  • RNA-seq QC, exploratory analysis, and enrichment workflows
  • Correlation networks and multi-omics integration
  • Dry-run-first automation patterns for safe public templates

Citation

If a repository is useful for your work, please cite the individual repository using its CITATION.cff metadata.

Popular repositories Loading

  1. 16s-qiime2-microbiome-pipeline 16s-qiime2-microbiome-pipeline Public

    Automated microbiome analysis workflow using QIIME2, PICRUSt2, LEfSe and network analysis in a Singularity environment.

  2. thermo-glycine-analysis thermo-glycine-analysis Public

    Reproducible analysis code and documentation for thermo-glycine 16S, RNA-seq, phenotype, and integration workflows.

    R

  3. omics-research-kit omics-research-kit Public

    Reproducible research notes, starter commands, and public resources for microbiome, shotgun metagenomics, transcriptomics, and proteomics workflows.

    Python

  4. asset-report-automation-methods asset-report-automation-methods Public

    Sanitized templates for asset-report collection and reproducibility workflows.

    Python

  5. yzyzero0098 yzyzero0098 Public

    Research profile README for reproducible omics workflows and automation templates.

  6. asset-analysis-loop-template asset-analysis-loop-template Public

    Sanitized template for synthetic asset-analysis automation loops.

    Python