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    • Gemma

      Public
      Genomics data re-analysis
      Java
      Apache License 2.0
      62335545Updated Apr 21, 2026Apr 21, 2026
    • gemma.R

      Public
      An R wrapper for the Gemma RESTful API
      R
      Apache License 2.0
      11090Updated Mar 31, 2026Mar 31, 2026
    • Python
      Other
      0000Updated Mar 19, 2026Mar 19, 2026
    • R
      0000Updated Mar 12, 2026Mar 12, 2026
    • Python
      0241Updated Mar 10, 2026Mar 10, 2026
    • RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
      Python
      The Unlicense
      525261Updated Mar 3, 2026Mar 3, 2026
    • GemBrow

      Public
      The Gemma Browser
      Vue
      Apache License 2.0
      14221Updated Feb 27, 2026Feb 27, 2026
    • baseCode

      Public
      Data structures, math and statistics tools, and utilities that are often needed across projects.
      Java
      Apache License 2.0
      0441Updated Feb 17, 2026Feb 17, 2026
    • Curated dependencies for the Pavlidis Lab's Java applications
      Apache License 2.0
      0041Updated Feb 15, 2026Feb 15, 2026
    • gsec

      Public
      Reusable implementation of the Spring Security framework for lab projects
      Java
      Apache License 2.0
      0037Updated Feb 4, 2026Feb 4, 2026
    • Code used for some analyses of data in Gemma. Probably not of general utility!
      Java
      0000Updated Jan 16, 2026Jan 16, 2026
    • rdp

      Public
      Researcher Gene Registry. Originally developed for the Canadian Rare Disease Models & Mechanisms Network
      Java
      Apache License 2.0
      751485Updated Jan 16, 2026Jan 16, 2026
    • gemmapy

      Public
      Python
      Apache License 2.0
      16112Updated Jan 9, 2026Jan 9, 2026
    • bioluigi

      Public
      Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
      Python
      Apache License 2.0
      0963Updated Jan 7, 2026Jan 7, 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
      04191Updated Dec 5, 2025Dec 5, 2025
    • R
      3600Updated Nov 20, 2025Nov 20, 2025
    • Downloads all all differential expression in Gemma for analysis
      R
      0020Updated 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
      2.4k000Updated Oct 20, 2025Oct 20, 2025
    • ermineJ

      Public
      Analysis of enrichment of gene sets with a GUI and CLI
      Java
      Apache License 2.0
      0020Updated Sep 3, 2025Sep 3, 2025
    • A theoretical study on the detection of dynamic gene regulation in bulk tissue transcriptomes.
      PostScript
      0000Updated Jun 29, 2025Jun 29, 2025
    • 0000Updated Jun 29, 2025Jun 29, 2025
    • TGEMO

      Public
      The Gemma Ontology
      Python
      1131Updated Jun 27, 2025Jun 27, 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
      124100Updated Jun 24, 2025Jun 24, 2025
    • aggtools

      Public
      R
      Other
      0010Updated Apr 29, 2025Apr 29, 2025
    • This repo contains the code for my paper on reproducible TR coexpression patterns using single cell RNA-seq
      R
      MIT License
      0000Updated 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
      05230Updated Apr 17, 2025Apr 17, 2025
    • ermineR

      Public
      R wrapper for ermineJ
      R
      Other
      4630Updated Apr 4, 2025Apr 4, 2025
    • Contains the code for "Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets"
      R
      MIT License
      1000Updated Mar 15, 2025Mar 15, 2025
    • This project looks to aggregate single cell coexpression patterns for microglial datasets
      R
      MIT License
      0000Updated Mar 14, 2025Mar 14, 2025
    • Leveraging data from the Unibind database.
      R
      0010Updated Mar 14, 2025Mar 14, 2025
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