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    68 repositories

    • Gemma

      Public
      Genomics data re-analysis
      bioinformaticsgenomics
      Java
      •
      Apache License 2.0
      •6•23•348•27•Updated Aug 3, 2025Aug 3, 2025

    • pavlab-starter-parent

      Public
      Curated dependencies for the Pavlidis Lab's Java applications
      Apache License 2.0
      •0•0•7•1•Updated Aug 3, 2025Aug 3, 2025

    • baseCode

      Public
      Data structures, math and statistics tools, and utilities that are often needed across projects.
      Java
      •
      Apache License 2.0
      •0•5•3•2•Updated Aug 3, 2025Aug 3, 2025

    • sc-annotation-pipeline

      Public
      Python
      •0•0•5•0•Updated Jul 30, 2025Jul 30, 2025

    • rnaseq-pipeline

      Public
      RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
      bashbioinformaticsrna-seqgenomicsngsgene-expressionbioinformatics-pipelinealignmentstarquantification
      Shell
      •
      The Unlicense
      •5•24•32•1•Updated Jul 29, 2025Jul 29, 2025

    • gsec

      Public
      Reusable implementation of the Spring Security framework for lab projects
      Java
      •
      Apache License 2.0
      •0•0•3•6•Updated Jul 29, 2025Jul 29, 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

    • GemBrow

      Public
      The Gemma Browser
      Vue
      •
      Apache License 2.0
      •1•4•29•1•Updated Jun 27, 2025Jun 27, 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
      •124•1•0•0•Updated Jun 24, 2025Jun 24, 2025

    • gemma.R

      Public
      An R wrapper for the Gemma RESTful API
      bioinformaticsgenomicstranscriptomicsgemma
      R
      •
      Apache License 2.0
      •1•10•9•0•Updated Jun 24, 2025Jun 24, 2025

    • gemmapy

      Public
      Python
      •
      Apache License 2.0
      •1•6•10•2•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•4•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

    • bioluigi

      Public
      Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
      bioinformaticsslurmgatkvcfannobcftoolsluigi-taskensembl-vep
      Python
      •
      Apache License 2.0
      •0•9•6•1•Updated Mar 18, 2025Mar 18, 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

    • ermineJ

      Public
      Analysis of enrichment of gene sets with a GUI and CLI
      bioinformaticsgenomicsbiologyenrichment-analysisgene-sets
      Java
      •
      Apache License 2.0
      •0•0•2•0•Updated Feb 13, 2025Feb 13, 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

    • neuroexpresso

      Public
      📊 Gene expression in neuroexpresso database
      visualizationbioinformaticsshinyneuroscienceneurobiologyneuroinformaticsneuronmancarci-2017neuroexpressor
      R
      •
      GNU General Public License v2.0
      •1•18•10•0•Updated Oct 25, 2024Oct 25, 2024

    • rdp

      Public
      Researcher Gene Registry. Originally developed for the Canadian Rare Disease Models & Mechanisms Network
      Java
      •
      Apache License 2.0
      •8•5•147•5•Updated Oct 9, 2024Oct 9, 2024

    • gotrack

      Public
      Web-based system and database that provides access to historical records and trends in the Gene Ontology and GO annotations
      Java
      •0•1•16•6•Updated Sep 25, 2024Sep 25, 2024

    • SFARI_project

      Public
      HTML
      •0•1•0•0•Updated Jun 26, 2024Jun 26, 2024

    • jenkins-replication-checksum

      Public
      Perform replication integrity checksum using Percona pt-table-checksum in a CI environment.
      Shell
      •
      MIT License
      •1•0•0•0•Updated May 2, 2024May 2, 2024