Repositories list

• themes

  Public
  Wordpress themes

  PHP

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

• ontomate-query-builder

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

• phenotype-annotation-pipeline

  Public
  Phenotype annotation pipeline, for mouse and human genes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

• rgd-web-application

  Public
  Code used by the RGD web site and tools

  JavaScript

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 2, 2025Jan 2, 2025

• ensembl-data-pipeline

  Public
  Load rat genes from Ensembl into RGD.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 2, 2025Jan 2, 2025

• rgd-core-library

  Public
  Domain layer and shared components

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 2, 2025Jan 2, 2025

• rgd-annotation-files

  Public
  GO annotation files in GAF, GPAD and GPI format

  GNU General Public License v3.0

  •0•0•1•0•Updated Dec 28, 2024Dec 28, 2024

• RDO-Disease-Ontology

  Public
  semantic-webhumanowl+ 5diseaseobomodel-organismsrdoontology

  0•0•1•0•Updated Dec 20, 2024Dec 20, 2024

• RS-Rat-Strain-Ontology

  Public
  Rat strain ontology maintained by RGD

  nomenclaturesemantic-webowl+ 9ontologyratoboontologiessymbolstrainobofoundry+ 2

  2•0•0•1•Updated Dec 20, 2024Dec 20, 2024

• XCO-Experimental-Condition-Ontology

  Public
  Experimental Condition Ontology maintained by RGD

  laboratorysemantic-webhuman+ 8owlontologyobomodel-organismsclinical-researchexperimental-conditionsobofoundry+ 1

  2•2•0•1•Updated Dec 20, 2024Dec 20, 2024

• MMO-Measurement-Method-Ontology

  Public
  Measurement method ontology maintained by RGD

  laboratorysemantic-webhuman+ 8owlontologymmoobomodel-organismsclinical-researchobofoundry+ 1

  2•1•0•1•Updated Dec 20, 2024Dec 20, 2024

• CMO-Clinical-Measurement-Ontology

  Public
  Clinical Measurement Ontology (CMO) maintained by RGD

  semantic-webhumanowl+ 7ontologyobomodel-organismscmoobofoundrylaboratory-measurementsclinical-measurements

  4•3•9•2•Updated Dec 20, 2024Dec 20, 2024

• interaction-counts-pipeline

  Public
  Computes "interactions count" for genes and proteins and and stores it in INTERACTION_COUNTS table.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• ontology-load-pipeline

  Public
  Load all ontologies used by RGD.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• text-mining-tools

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• qtl-rso-annotation-pipeline

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• ctd-disease-annotation-pipeline

  Public
  Load disease annotations to genes based on CTD FTP files.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• gff3-pipeline

  Public
  Creates gff3 files to be loaded into RGD JBrowse instance.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• eva-pipeline

  Public
  Load variants from EVA for Rat, Dog, Green Monkey, Mouse, and Pig.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• variant-load-pipeline

  Public
  Load rat strain data from VCF files into RGD database and precomputes data for use by Variant Visualizer tool

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

• hgnc-pipeline

  Public
  Handles obsolete HGNC IDs for human genes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

• misc-tools

  Public
  Miscellaneous tools, often one-off.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• rna-central-pipeline

  Public
  Import RNACentral IDs as 'external database ids' for all non-coding genes in RGD to generate links to RNACentral database.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

• static-site-content

  Public
  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

• rgd-web-services

  Public
  Swagger implementation

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• marker-load-pipeline

  Public
  Load the marker data for new assembly

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• human-proteome-map-pipeline

  Public
  Load Human Proteome Map ids for human genes

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• phenogen-pipeline

  Public
  Load external database ids to PhenoGen database at UC Denver.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• alliance-submission-pipeline

  Public
  Generate and submit files for rat and human to the Alliance (https://www.alliancegenome.org/)

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• expression-tpm-pipeline

  Public
  load the TPM data being generated for GEO expression samples

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 2, 2024Dec 2, 2024