rat-genome-database Goto Github PK

alliance-submission-pipeline

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

array-id-import-pipeline

Import array ids with synergizer

biocyc-pipeline

cellosaurus-pipeline

Pipeline to import cell lines from cellosaurus at Expasy

cgi-site-content

chromosome-pipeline

Load chromosome and cytoband information.

clinvar-pipeline

Loads variants from ClinVar into RGD database. Creates disease annotations to variants and also for genes, based on orthology.

cmo-clinical-measurement-ontology

Clinical Measurement Ontology (CMO) maintained by RGD

cosmic-pipeline

cs-chinchilla-sources-ontology

Chinchilla sources ontology maintained by RGD

ctd-chem-drug-pipeline

Imports chemical annotations from CTD database.

ctd-disease-annotation-pipeline

Load disease annotations to genes based on CTD FTP files.

data-qc-pipeline

General purpose qc reports on data integrity.

db-snp-pipeline

Load DB_SNP into db.

disease-navigator

elastic-search-indexer-pipeline

Pipeline to create elastic search indexes.

ensembl-data-pipeline

Load rat genes from Ensembl into RGD.

ensembl-pipeline

Downloads genes from Ensembl and compares them against genes in RGD.

epd-pipeline

Load rat, human, mouse and dog promoters from EPD (Eucaryotic Promoter Database)

europe-pmc-pipeline

Generate a XML file to send to Europe PMC

eva-pipeline

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

expression-load-pipeline

Pipeline to load experiment values from expression atlas

fix-duplicate-ref-rgd_ids-pipeline

Fixes the problem of duplicate PubMed ids for references

ftp-file-extracts-pipeline

Generate weekly files for RGD FTP site

full-annot-index-pipeline

Updates FULL_ANNOT_INDEX table: big auxiliary table used to speed up many annotation queries used by RGD tools.

full-record-index-pipeline

Precomputes summaries from experiment record data into FULL_RECORD_INDEX table for subsequent use by phenominer tool.

gene-description-pipeline

Generate gene descriptions for rat, mouse nad human based on automated gene synopses from AGR merged with automated gene synopses from RGD.

gene-loading-pipeline

Loads gene models from NCBI

gene-loci-pipeline

Populates GENE_LOCI table used by Variant Visualizer tool.

generalsearch

general search legacy web app