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16 followers · 22 following

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Achievement: Pull Sharkx3Achievement: QuickdrawAchievement: Pair ExtraordinaireAchievement: YOLOAchievement: StarstruckAchievement: Arctic Code Vault Contributor

Achievements

Achievement: Pull Sharkx3Achievement: QuickdrawAchievement: Pair ExtraordinaireAchievement: YOLOAchievement: StarstruckAchievement: Arctic Code Vault Contributor

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ToledoEM/README.md

Hola 👋 This is my GitHub

  • 🧬 Scientist trained in cellular and molecular biology, mostly working on genomics, neurobiology, development, and cardio-metabolism across tissues.
  • 🧪 Genomics practitioner by background, wet lab, computational analysis.
  • 🖥️ I approach biological questions through Computational and Systems biology.
  • 🔩 Applying ML/AI in biological problems.
  • 🏛️ Experience across academia and research in industry.
  • 🤝 Strong believer in academic–industry collaboration: publications, student supervision, internships, and research partnerships.
  • 📚 Publications
  • 💼 LinkedIn
  • 👾 Website

Science stuff: Statistical tools and reproducible analysis

  • e-means - R (and Rust) implementation of super fast clustering method for big datasets e-means
  • xkcd – XKCD hand-drawn ggplot2 aesthetics
  • PubMatrixR-v2 – PubMed co-occurrence matrices Also for python
  • msigdf – tidy MSigDB gene sets
  • Bash-blind-rename – bias-free file renaming for manual image quantification

Semi-Scientific

  • linXiv-web - Unofficial linXiv component for self-hosting and a web UI. Papers - pdf - manager for self-hosting (a reference manager in the making)

Utilities, automation, and self-hosting.

Home Assistant
Others

These repositories are for fun, other for science and a few more for very specific solutions

Send me an email, connect on LinkedIn, or read more about my work and side projects.

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  1. msigdf msigdf Public

    Forked from stephenturner/msigdf

    Molecular Signatures Database (MSigDB) in a tidy data frame

    R 27 5

  2. xkcd xkcd Public

    This R package facilitates hand-drawn XKCD-style graphics using ggplot2 through custom geometric objects for jittered lines, segments, circles, and figures that capture the XKCD aesthetic. Compatib…

    HTML 4 1

  3. PubMatrixR-v2 PubMatrixR-v2 Public

    PubMatrixR is an R package that performs systematic literature searches on PubMed and PMC databases using pairwise combinations of search terms. It creates co-occurrence matrices showing the number…

    R 1

  4. emeansR emeansR Public

    10X faster clustering method for big datasets. An R implementation of e-means (Bessa et al., 2026)

    R

  5. linXiv-web linXiv-web Public

    Unofficial linXiv component for seflhosting and a web UI

    Python 3

  6. Bash-blind-rename Bash-blind-rename Public

    Rename files on folder for manual image blind analysis to avoid bias.

    Shell 1