genomicsengland Goto Github PK

gel_stack_overflow

A Stack Overflow clone for teams (self-hosted)

gel_to_opentargets

Scripts for transforming Genomics England data into a form suitable for Open Targets

gitlab-test

test repo for gitlab

gmcs

gms-consent-inspections

Create JIRA tickets with GMS consent form snippets to check against data submitted by GLHs

gms-duplicate-person-search

Search for duplicate participants within the NGIS databases

gms_rr_data_dictionary

Generate data dictionary for GMS research release

gmslabkey

gyda

A tool to map short free text to phenotypic ontology terms

hgvs

HGVS variant name parsing and generation

how-to-git

Git repo to show how to use fetch/rebase/review PRs like a boss

index_migration

Scripts used to QC migraiton of EDS Index database

inuvika

jca_cfdna_project_code

code for matching WGS samples to cfDNA samples, based on containing certain key genes in the tiering file

jca_checking_which_files_are_associated_with_which_studies

jca_miscellaneous_functions

jira-tests

Jira Automated Tests

juli

Junction Location Identifier (JuLI): DNA fusion detection tool for clinical sequencing.

jwtgenerator

make_erd

Python script to auto-generate ER diagrams from database connections

mftgoanywhere

minimal_subset_genomic_dataset

Minimal Nextflow pipeline to test genomic data processing in Cloud-RE

ngis-mq-report

R and Rmd scripts for the generation of reports off the back of NGIS MQ

nhsd_application

nhse_contractural_metrics

ETLs to generate the contractural metrics for distribution to GLHs and NHSE https://cnfl.extge.co.uk/display/CDT/NHS+Contractural+Metrics

openshift-ansible-skeleton

panelapp

Genomics England PanelApp - A crowdsourcing tool to allow gene panels to be shared, downloaded, viewed and evaluated by the Scientific Community

patient-level-contract-monitoring

Dataset used to monitor, at a sample level, the activity undertaken through the GMS pipeline. For submission to NHSE.

pc-docker-clamav

Dockerized open source antivirus for use with file sharing containers, REST API or TCP.

pedigree-audit-mock

Pedigree Panel Mock Facade