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@PavlidisLab Pavlidis lab

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    74 repositories

    • Gemma

      Public
      Genomics data re-analysis
      bioinformaticsgenomics
      bioinformaticsgenomics
      Java
      •
      Apache License 2.0
      •6•24•244•43•Updated Oct 12, 2026Oct 12, 2026

    • gemma-ui

      Public
      Modernised React + TypeScript curation interface for the Gemma database. Drives the curation REST API and integrates agent-proposed designs / tags.
      TypeScript
      •
      Apache License 2.0
      •0•0•4•1•Updated Oct 10, 2026Oct 10, 2026

    • gemma.R

      Public
      An R wrapper for the Gemma RESTful API
      bioinformaticsgenomicstranscriptomics
      bioinformaticsgenomicstranscriptomicsgemma
      R
      •
      Apache License 2.0
      •1•10•9•0•Updated Oct 3, 2026Oct 3, 2026

    • sc-annotation-pipeline

      Public
      Python
      •
      Other
      •0•3•4•0•Updated Oct 2, 2026Oct 2, 2026

    • gemmapy

      Public
      Python
      •
      Apache License 2.0
      •1•7•11•3•Updated Oct 2, 2026Oct 2, 2026

    • TGEMO

      Public
      The Gemma Ontology
      Python
      •1•1•3•1•Updated Sep 16, 2026Sep 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.
      Python
      •
      Other
      •0•2•0•0•Updated Sep 3, 2026Sep 3, 2026

    • Pseudobulk_Function_Pipeline

      Public
      Jupyter Notebook
      •0•0•1•0•Updated Aug 31, 2026Aug 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.
      Python
      •
      Other
      •0•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • rnaseq-pipeline

      Public
      RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
      bashbioinformaticsrna-seq
      bashbioinformaticsrna-seqgenomicsngsgene-expressionbioinformatics-pipelinealignmentstarquantification
      Python
      •
      The Unlicense
      •4•25•26•1•Updated Jul 22, 2026Jul 22, 2026

    • bioluigi

      Public
      Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
      bioinformaticsslurmgatk
      bioinformaticsslurmgatkvcfannobcftoolsluigi-taskensembl-vep
      Python
      •
      Apache License 2.0
      •0•9•6•3•Updated Jul 10, 2026Jul 10, 2026

    • rdp

      Public
      Researcher Gene Registry. Originally developed for the Canadian Rare Disease Models & Mechanisms Network
      Java
      •
      Apache License 2.0
      •7•5•149•5•Updated Jun 16, 2026Jun 16, 2026

    • baseCode

      Public
      Data structures, math and statistics tools, and utilities that are often needed across projects.
      Java
      •
      Apache License 2.0
      •0•4•4•1•Updated Jun 5, 2026Jun 5, 2026

    • GPT_annotate

      Public
      R
      •0•0•0•0•Updated Jun 4, 2026Jun 4, 2026

    • pavlab-starter-parent

      Public
      Curated dependencies for the Pavlidis Lab's Java applications
      Apache License 2.0
      •0•0•4•2•Updated May 20, 2026May 20, 2026

    • Persistent-Hindrances-to-Data-Re-use-in-Single-Cell-Genomics

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • GemBrow

      Public
      The Gemma Browser
      Vue
      •
      Apache License 2.0
      •1•4•22•1•Updated Feb 27, 2026Feb 27, 2026

    • gsec

      Public
      Reusable implementation of the Spring Security framework for lab projects
      Java
      •
      Apache License 2.0
      •0•0•3•7•Updated Feb 4, 2026Feb 4, 2026

    • GemmaAnalysis

      Public
      Code used for some analyses of data in Gemma. Probably not of general utility!
      Java
      •0•0•0•0•Updated Jan 16, 2026Jan 16, 2026

    • ndb

      Public
      Web application and database providing a harmonized and comprehensive collection of genetic variants published in peer-reviewed literature.
      Java
      •
      Apache License 2.0
      •0•4•19•1•Updated Dec 5, 2025Dec 5, 2025

    • regenerationCMap

      Public
      R
      •3•6•0•0•Updated Nov 20, 2025Nov 20, 2025

    • gemmaDifExpDump

      Public
      Downloads all all differential expression in Gemma for analysis
      R
      •0•0•2•0•Updated Nov 4, 2025Nov 4, 2025

    • luigi

      Public
      Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also…
      Python
      •
      Apache License 2.0
      •2.5k•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • ermineJ

      Public
      Analysis of enrichment of gene sets with a GUI and CLI
      bioinformaticsgene-setsgenomics
      bioinformaticsgene-setsgenomicsbiologyenrichment-analysis
      Java
      •
      Apache License 2.0
      •0•0•2•0•Updated Sep 3, 2025Sep 3, 2025

    • coex-simulation

      Public
      A theoretical study on the detection of dynamic gene regulation in bulk tissue transcriptomes.
      PostScript
      •0•0•0•0•Updated Jun 29, 2025Jun 29, 2025

    • simulation

      Public
      0•0•0•0•Updated Jun 29, 2025Jun 29, 2025

    • RSEM

      Public
      RSEM with STAR shared memory support (fork from RSEM: accurate quantification of gene and isoform expression from RNA-Seq data)
      C++
      •
      GNU General Public License v3.0
      •122•1•0•0•Updated Jun 24, 2025Jun 24, 2025

    • aggtools

      Public
      R
      •
      Other
      •0•0•1•0•Updated Apr 29, 2025Apr 29, 2025

    • TR_singlecell

      Public
      This repo contains the code for my paper on reproducible TR coexpression patterns using single cell RNA-seq
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

    • GemmaDE

      Public
      Discover biological conditions associated with differential gene expression by compiling information from >10,000 published experiments
      R
      •
      MIT License
      •0•5•23•0•Updated Apr 17, 2025Apr 17, 2025
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