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@PavlidisLab

Pavlidis lab

The Pavlidis Lab at the University of British Columbia

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  1. Gemma Gemma Public

    Genomics data re-analysis

    Java 24 6

  2. markerGeneProfile markerGeneProfile Public

    Marker gene profile estimation method used in NeuroExpresso manuscript

    R 14 2

  3. neuroexpresso neuroexpresso Public

    📊 Gene expression in neuroexpresso database

    R 18 1

Repositories

Showing 10 of 74 repositories
  • gemma.R Public

    An R wrapper for the Gemma RESTful API

    PavlidisLab/gemma.R's past year of commit activity
    R 10 Apache-2.0 1 9 0 Updated Oct 3, 2026
  • sc-annotation-pipeline Public
    PavlidisLab/sc-annotation-pipeline's past year of commit activity
    Python 3 0 4 0 Updated Oct 2, 2026
  • gemma-ui Public

    Modernised React + TypeScript curation interface for the Gemma database. Drives the curation REST API and integrates agent-proposed designs / tags.

    PavlidisLab/gemma-ui's past year of commit activity
    TypeScript 0 Apache-2.0 0 4 1 Updated Oct 2, 2026
  • Gemma Public

    Genomics data re-analysis

    PavlidisLab/Gemma's past year of commit activity
    Java 24 Apache-2.0 6 244 43 Updated Oct 2, 2026
  • gemmapy Public
    PavlidisLab/gemmapy's past year of commit activity
    Python 7 Apache-2.0 1 11 3 Updated Oct 2, 2026
  • TGEMO Public

    The Gemma Ontology

    PavlidisLab/TGEMO's past year of commit activity
    Python 1 1 3 1 Updated Sep 16, 2026
  • gemma-curation-benchmark-data Public

    Human-curated gold-standard Gemma curation (factors + tags) for benchmarking automated curation. Dev set = 400; test100 to follow. CC BY-NC 4.0.

    PavlidisLab/gemma-curation-benchmark-data's past year of commit activity
    Python 1 0 0 0 Updated Sep 3, 2026
  • Pseudobulk_Function_Pipeline Public
    PavlidisLab/Pseudobulk_Function_Pipeline's past year of commit activity
    Jupyter Notebook 0 0 1 0 Updated Aug 31, 2026
  • gemma-curation-agents-v1.1 Public

    Gemma curation agents — v1.1 frozen public-release snapshot (paper-pinned). Agentic pipeline proposing/auditing Gemma curation for curator review.

    PavlidisLab/gemma-curation-agents-v1.1's past year of commit activity
    Python 0 0 0 0 Updated Jul 30, 2026
  • rnaseq-pipeline Public

    RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

    PavlidisLab/rnaseq-pipeline's past year of commit activity
    Python 25 Unlicense 4 26 1 Updated Jul 22, 2026
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