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    • gemma.R

      Public
      An R wrapper for the Gemma RESTful API
      R
      Apache License 2.0
      11080Updated Nov 27, 2024Nov 27, 2024
    • Gemma

      Public
      Genomics data re-analysis
      Java
      Apache License 2.0
      62331629Updated Nov 22, 2024Nov 22, 2024
    • R
      MIT License
      0000Updated Nov 5, 2024Nov 5, 2024
    • Curated dependencies for the Pavlidis Lab's Java applications
      Apache License 2.0
      0071Updated Nov 2, 2024Nov 2, 2024
    • RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
      Python
      The Unlicense
      422301Updated 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
      0532Updated Oct 25, 2024Oct 25, 2024
    • TGEMO

      Public
      The Gemma Ontology
      Python
      1131Updated Oct 25, 2024Oct 25, 2024
    • 📊 Gene expression in neuroexpresso database
      R
      GNU General Public License v2.0
      118100Updated Oct 25, 2024Oct 25, 2024
    • ermineR

      Public
      R wrapper for ermineJ
      R
      Other
      4630Updated 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
      851445Updated Oct 9, 2024Oct 9, 2024
    • GemBrow

      Public
      The Gemma Browser
      Vue
      Apache License 2.0
      14271Updated 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
      01166Updated Sep 25, 2024Sep 25, 2024
    • A theoretical study on the detection of dynamic gene regulation in bulk tissue transcriptomes.
      PostScript
      Apache License 2.0
      0000Updated Sep 23, 2024Sep 23, 2024
    • ermineJ

      Public
      Analysis of enrichment of gene sets with a GUI and CLI
      Java
      Apache License 2.0
      0020Updated 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
      04191Updated Sep 18, 2024Sep 18, 2024
    • bioluigi

      Public
      Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
      Python
      Apache License 2.0
      0961Updated Aug 19, 2024Aug 19, 2024
    • gemmapy

      Public
      Python
      Apache License 2.0
      1682Updated Aug 8, 2024Aug 8, 2024
    • gsec

      Public
      Reusable implementation of the Spring Security framework for lab projects
      Java
      Apache License 2.0
      0036Updated Jul 26, 2024Jul 26, 2024
    • HTML
      0100Updated Jun 26, 2024Jun 26, 2024
    • Perform replication integrity checksum using Percona pt-table-checksum in a CI environment.
      Shell
      MIT License
      1000Updated May 2, 2024May 2, 2024
    • Downloads all all differential expression in Gemma for analysis
      R
      0020Updated 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
      119100Updated Mar 13, 2024Mar 13, 2024
    • Functions to store and access backups of Gemma API outputs
      R
      0010Updated Feb 22, 2024Feb 22, 2024
    • Contains the code for "Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets"
      R
      MIT License
      0000Updated Feb 4, 2024Feb 4, 2024
    • Leveraging data from the Unibind database.
      R
      0010Updated Nov 10, 2023Nov 10, 2023
    • Code used for some analyses of data in Gemma. Probably not of general utility!
      Java
      0000Updated 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
      0401Updated Oct 26, 2023Oct 26, 2023
    • R
      0010Updated 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
      04230Updated Aug 10, 2023Aug 10, 2023
    • 0000Updated Apr 17, 2023Apr 17, 2023