Repositories list

• Gemma

  Public
  Genomics data re-analysis

  bioinformaticsgenomics

  Java

  •

  Apache License 2.0

  •6•23•330•31•Updated Jun 21, 2025Jun 21, 2025

• gemma.R

  Public
  An R wrapper for the Gemma RESTful API

  bioinformaticsgenomicstranscriptomics+ 1gemma

  R

  •

  Apache License 2.0

  •1•10•9•0•Updated Jun 19, 2025Jun 19, 2025

• sc-annotation-pipeline

  Public
  Python

  •0•0•5•0•Updated Jun 16, 2025Jun 16, 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 Jun 6, 2025Jun 6, 2025

• GemBrow

  Public
  The Gemma Browser

  Vue

  •

  Apache License 2.0

  •1•4•28•1•Updated Jun 6, 2025Jun 6, 2025

• gemmapy

  Public
  Python

  •

  Apache License 2.0

  •1•6•9•2•Updated May 28, 2025May 28, 2025

• gsec

  Public
  Reusable implementation of the Spring Security framework for lab projects

  Java

  •

  Apache License 2.0

  •0•0•3•6•Updated May 15, 2025May 15, 2025

• pavlab-starter-parent

  Public
  Curated dependencies for the Pavlidis Lab's Java applications

  Apache License 2.0

  •0•0•7•1•Updated May 12, 2025May 12, 2025

• aggtools

  Public
  R

  •

  Other

  •0•0•1•0•Updated Apr 29, 2025Apr 29, 2025

• rnaseq-pipeline

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

  bashbioinformaticsrna-seq+ 15genomicsngsgene-expressionbioinformatics-pipelinealignmentstarquantification+ 8

  Shell

  •

  The Unlicense

  •5•24•31•1•Updated Apr 28, 2025Apr 28, 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-setsgenomics+ 3biologyenrichment-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

  bioinformaticsslurmgatk+ 4vcfannobcftoolsluigi-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

• TGEMO

  Public
  The Gemma Ontology

  Python

  •1•1•3•1•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

  bioinformaticsgenomicsbiology+ 2enrichment-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

  visualizationbioinformaticsshiny+ 8neuroscienceneurobiologyneuroinformaticsneuronmancarci-2017neuroexpressor+ 1

  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

• coex-simulation

  Public
  A theoretical study on the detection of dynamic gene regulation in bulk tissue transcriptomes.

  PostScript

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 23, 2024Sep 23, 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

• gemmaDifExpDump

  Public
  Downloads all all differential expression in Gemma for analysis

  R

  •0•0•2•0•Updated Apr 12, 2024Apr 12, 2024

• 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

  •123•1•0•0•Updated Mar 13, 2024Mar 13, 2024