Repositories list

• Gemma

  Public
  Genomics data re-analysis

  bioinformaticsgenomics

  Java

  •

  Apache License 2.0

  •6•23•315•29•Updated Nov 22, 2024Nov 22, 2024

• TR_singlecell

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• pavlab-starter-parent

  Public
  Curated dependencies for the Pavlidis Lab's Java applications

  Apache License 2.0

  •0•0•7•1•Updated Nov 2, 2024Nov 2, 2024

• rnaseq-pipeline

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

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

  Python

  •

  The Unlicense

  •4•22•30•1•Updated Oct 28, 2024Oct 28, 2024

• 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 Oct 25, 2024Oct 25, 2024

• TGEMO

  Public
  The Gemma Ontology

  Python

  •1•1•3•1•Updated Oct 25, 2024Oct 25, 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

• gemma.R

  Public
  An R wrapper for the Gemma RESTful API

  bioinformaticsgenomicstranscriptomics+ 1gemma

  R

  •

  Apache License 2.0

  •1•10•8•0•Updated Oct 22, 2024Oct 22, 2024

• ermineR

  Public
  R wrapper for ermineJ

  bioinformaticsgene-setsgenomics+ 3biologyenrichment-analysisogan-bio

  R

  •

  Other

  •4•6•3•0•Updated Oct 15, 2024Oct 15, 2024

• rdp

  Public
  Researcher Gene Registry. Originally developed for the Canadian Rare Disease Models & Mechanisms Network

  Java

  •

  Apache License 2.0

  •8•5•144•5•Updated Oct 9, 2024Oct 9, 2024

• GemBrow

  Public
  The Gemma Browser

  Vue

  •

  Apache License 2.0

  •1•4•27•1•Updated Oct 5, 2024Oct 5, 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

• 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 Sep 18, 2024Sep 18, 2024

• 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 Sep 18, 2024Sep 18, 2024

• 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 Aug 19, 2024Aug 19, 2024

• gemmapy

  Public
  Python

  •

  Apache License 2.0

  •1•6•8•2•Updated Aug 8, 2024Aug 8, 2024

• gsec

  Public
  Reusable implementation of the Spring Security framework for lab projects

  Java

  •

  Apache License 2.0

  •0•0•3•6•Updated Jul 26, 2024Jul 26, 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

  •119•1•0•0•Updated Mar 13, 2024Mar 13, 2024

• gemmaBackups

  Public
  Functions to store and access backups of Gemma API outputs

  R

  •0•0•1•0•Updated Feb 22, 2024Feb 22, 2024

• 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

  •0•0•0•0•Updated Feb 4, 2024Feb 4, 2024

• Unibind_analysis

  Public
  Leveraging data from the Unibind database.

  R

  •0•0•1•0•Updated Nov 10, 2023Nov 10, 2023

• GemmaAnalysis

  Public
  Code used for some analyses of data in Gemma. Probably not of general utility!

  Java

  •0•0•0•0•Updated Oct 26, 2023Oct 26, 2023

• aspiredb

  Public
  ASPIREdb is a web-based software system for the analysis of genomic variants (CNVs, SNVs, and Indels) and phenotypes. Potential users include researchers who are trying to understand the relationships between discovered variants and phenotypes.

  JavaScript

  •

  Apache License 2.0

  •0•4•0•1•Updated Oct 26, 2023Oct 26, 2023

• regenerationCMap

  Public
  R

  •0•0•1•0•Updated Oct 21, 2023Oct 21, 2023

• 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 Aug 10, 2023Aug 10, 2023

• pavlab-parent

  Public
  0•0•0•0•Updated Apr 17, 2023Apr 17, 2023