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Achievement: Pull Sharkx2Achievement: QuickdrawAchievement: StarstruckAchievement: YOLOAchievement: Pair Extraordinaire

Achievements

Achievement: Pull Sharkx2Achievement: QuickdrawAchievement: StarstruckAchievement: YOLOAchievement: Pair Extraordinaire

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tunabirgun/README.md

Tuna Birgün

Computational biology, transcriptomics, genomics and reproducible scientific software.

MSc Biotechnology, Istanbul Technical University · Research Assistant, Istanbul Yeni Yuzyil University

Website · Email · ORCID · LinkedIn

I work on expression analysis, functional genomics and single-cell workflows, including crops, filamentous fungi and yeasts with limited annotation. I build research tools in R, Python and desktop/web frameworks, with an emphasis on reproducibility and interfaces that expose the evidence behind a result.

Selected projects

Project Purpose
BulkSeq Studio Desktop bulk RNA-seq and microarray analysis for Windows and Linux
TEagle Transposable-element evaluation and PCR assay planning
Omicau Multi-omics input auditing and predictive assay-contribution comparisons
Arf Markdown notes, references and on-device related-note discovery
Litehouse Browser-local literature discovery and Markdown evidence reports; web alpha

I also write in Turkish and English about epistemology, scientific methodology and the history of science at tunabirgun.com.

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  1. bulkseq-studio bulkseq-studio Public

    Cross-platform (Windows + Linux) no-code desktop app for reproducible bulk RNA-seq & microarray analysis: STAR/HISAT2/Salmon alignment, DESeq2/limma, GO/KEGG/g:Profiler enrichment, and STRING PPI n…

    Python 1

  2. TEagle TEagle Public

    Evidence-traceable Windows desktop app for transposable-element (TE) annotation and TE-aware, genome-validated PCR primer design. Native PySide6/Qt, offline scientific core, optional one-click Dfam…

    Python 1

  3. arf arf Public

    A local-first second brain for scientists, researchers, coders, and nerds.

    Svelte 25 2

  4. litehouse litehouse Public

    Litehouse: local-first literature surveillance and evidence reporting.

    TypeScript

  5. omicau omicau Public

    Local multi-omics input auditing, predictive comparisons and paired assay-contribution reporting via CLI and browser.

    Python

  6. rewired rewired Public

    R pipeline for identifying systems-level network rewiring and functional defense modules in Fusarium species using differential interactome analysis.

    R 1