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    69 repositories

    • Gemma

      Public
      Genomics data re-analysis
      bioinformaticsgenomics
      Java
      •
      Apache License 2.0
      •6•23•356•38•Updated Dec 1, 2025Dec 1, 2025

    • rnaseq-pipeline

      Public
      RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
      bashbioinformaticsrna-seqgenomicsngsgene-expressionbioinformatics-pipelinealignmentstarquantification
      Python
      •
      The Unlicense
      •5•24•21•1•Updated Nov 27, 2025Nov 27, 2025

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

      Public
      Python
      •0•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • sc-annotation-pipeline

      Public
      Python
      •0•1•4•2•Updated Nov 22, 2025Nov 22, 2025

    • regenerationCMap

      Public
      R
      •2•4•0•0•Updated Nov 20, 2025Nov 20, 2025

    • bioluigi

      Public
      Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
      bioinformaticsslurmgatkvcfannobcftoolsluigi-taskensembl-vep
      Python
      •
      Apache License 2.0
      •0•9•6•3•Updated Nov 17, 2025Nov 17, 2025

    • gemmapy

      Public
      Python
      •
      Apache License 2.0
      •1•6•11•2•Updated Nov 13, 2025Nov 13, 2025

    • GemBrow

      Public
      The Gemma Browser
      Vue
      •
      Apache License 2.0
      •1•4•22•1•Updated Nov 4, 2025Nov 4, 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 comes with Hadoop support built in.
      Python
      •
      Apache License 2.0
      •2.4k•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • gemma.R

      Public
      An R wrapper for the Gemma RESTful API
      bioinformaticsgenomicstranscriptomicsgemma
      R
      •
      Apache License 2.0
      •1•10•10•0•Updated Oct 9, 2025Oct 9, 2025

    • baseCode

      Public
      Data structures, math and statistics tools, and utilities that are often needed across projects.
      Java
      •
      Apache License 2.0
      •0•4•4•2•Updated Oct 9, 2025Oct 9, 2025

    • pavlab-starter-parent

      Public
      Curated dependencies for the Pavlidis Lab's Java applications
      Apache License 2.0
      •0•0•4•1•Updated Oct 9, 2025Oct 9, 2025

    • gsec

      Public
      Reusable implementation of the Spring Security framework for lab projects
      Java
      •
      Apache License 2.0
      •0•0•3•6•Updated Sep 17, 2025Sep 17, 2025

    • ermineJ

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

    • rdp

      Public
      Researcher Gene Registry. Originally developed for the Canadian Rare Disease Models & Mechanisms Network
      Java
      •
      Apache License 2.0
      •7•5•148•5•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

    • TGEMO

      Public
      The Gemma Ontology
      Python
      •1•1•3•1•Updated 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
      •126•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

    • GemmaAnalysis

      Public
      Code used for some analyses of data in Gemma. Probably not of general utility!
      Java
      •0•0•0•0•Updated Apr 18, 2025Apr 18, 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

    • ermineR

      Public
      R wrapper for ermineJ
      bioinformaticsgene-setsgenomicsbiologyenrichment-analysisogan-bio
      R
      •
      Other
      •4•6•3•0•Updated Apr 4, 2025Apr 4, 2025

    • TR_aggregation

      Public
      Contains the code for "Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets"
      R
      •
      MIT License
      •1•0•0•0•Updated Mar 15, 2025Mar 15, 2025

    • aggregate_microglia

      Public
      This project looks to aggregate single cell coexpression patterns for microglial datasets
      R
      •
      MIT License
      •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

    • Unibind_analysis

      Public
      Leveraging data from the Unibind database.
      R
      •0•0•1•0•Updated Mar 14, 2025Mar 14, 2025

    • owlviz

      Public
      A Protégé Desktop plugin that provides a graphical representation of the class hierarchy in an OWL ontology.
      Java
      •12•0•0•0•Updated Feb 24, 2025Feb 24, 2025

    • 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 12, 2024Dec 12, 2024