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@YeoLab

Yeo lab at UCSD

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  1. flotilla flotilla Public archive

    Reproducible machine learning analysis of gene expression and alternative splicing data

    Jupyter Notebook 125 25

  2. single-cell-bioinformatics single-cell-bioinformatics Public archive

    Course material in notebook format for learning about single cell bioinformatics methods

    Jupyter Notebook 100 38

  3. bento-tools bento-tools Public

    A Python toolkit for subcellular analysis of spatial transcriptomics data

    Python 86 7

  4. clipper clipper Public

    A tool to identify CLIP-seq peaks

    Python 70 44

  5. outrigger outrigger Public

    Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data

    Python 67 22

  6. sailor sailor Public archive

    CWL+Singularity implementation of an RNA editing workflow

    Jupyter Notebook 40 11

Repositories

Showing 10 of 70 repositories
  • skipper Public

    Skip the peaks and expose RNA-binding in CLIP data

    YeoLab/skipper’s past year of commit activity
    Python 10 5 3 2 Updated Jan 27, 2026
  • chim-eCLIP Public

    chimeric eCLIP processing pipeline

    YeoLab/chim-eCLIP’s past year of commit activity
    Common Workflow Language 4 MIT 1 0 0 Updated Jan 27, 2026
  • encode_analysis Public

    ENCODE paper analysis 2025 (Charlene)

    YeoLab/encode_analysis’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Dec 29, 2025
  • MARINE Public

    MARINE: Multi-core Algorithm for Rapid Identification of Nucleotide Edits

    YeoLab/MARINE’s past year of commit activity
    Jupyter Notebook 2 MIT 1 3 0 Updated Nov 20, 2025
  • bento-tools Public

    A Python toolkit for subcellular analysis of spatial transcriptomics data

    YeoLab/bento-tools’s past year of commit activity
    Python 86 BSD-2-Clause 7 15 1 Updated Nov 16, 2025
  • clipper Public

    A tool to identify CLIP-seq peaks

    YeoLab/clipper’s past year of commit activity
    Python 70 44 52 2 Updated Oct 31, 2025
  • metadata-db Public archive
    YeoLab/metadata-db’s past year of commit activity
    Less 0 0 4 1 Updated Sep 10, 2025
  • Yeo_RNA_base_editing Public

    Smargon et. al, "Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs"

    YeoLab/Yeo_RNA_base_editing’s past year of commit activity
    0 1 0 0 Updated Aug 6, 2025
  • containers Public

    Collection of Dockerfiles

    YeoLab/containers’s past year of commit activity
    Dockerfile 0 1 1 0 Updated Jul 30, 2025
  • Mudskipper Public
    YeoLab/Mudskipper’s past year of commit activity
    Python 1 1 2 0 Updated May 8, 2025

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