Discover MRCIEU/BiobankPhenotypes Open Source project

Awesome list for all things AI, ML and deep learning

awesome-ai

gwas2vcf

Convert GWAS summary statistics to VCF

Data objects for various sets of instruments

MRInstruments

epigraphdb-pqtl

This is the github repository to provide the R scripts been used in the phenome-wide Mendelian randomization study of plasma proteome.

Health-and-Wellbeing-MR

epigraphdb

Examples on using EpiGraphDB

a pipeline of metabolomics data processing and quality control

epigraphdb-r

R package for epigraphdb

metaboprep

gwas-vcf-specification

Specification for the GWAS-VCF format (manuscript in preparation)

gwasglue2

Connecting GWAS summary data to analytical tools

PhenoSpD

MELODI-Presto

A fast and programmatic MELODI

Notes and code for running UK Biobank GWAS at the MRC IEU

UKBiobankGWAS

A tool for analysing continuous glucose monitoring (CGM) data in epidemiology.

godmc

GoDMC analysis pipeline

PHESANT-MR-pheWAS-BMI

GLU

ieugwaspy

Python interface to the MRC IEU GWAS database API

Pipeline for genetic epidemiology projects at Univsersity of Bristol

GeneHackman

genetics.binaRies

Binaries for tools used in genetics in an R package

vectology

Using language models and ontology topology to perform semantic mapping of traits between biomedical datasets

Python library for reading GWAS summary statistics in GWAS-VCF files

CheckSumStats

pygwasvcf

Mining Enriched Literature Objects to Derive Intermediates

melodi

Scripts to run mQTL analyses as described in the ARIES mQTL paper

ariesmqtl

Multi-ancestry MR of blood pressure drug targets

bp-drug-mr

Text mining for mechanism prioritisation

temmpo

godmc_phase2_analysis

Manhattan plot function which highlights SNPs in different colours

qqman_multiple_colours

UKBActivityBoutLength

Assessing association of physical activity types and bout length in UK Biobank

mrbase_casestudies

Using the MR-Base platform to investigate risk factors and drug targets for thousands of phenotypes

introduction-to-r

API for MRC-IEU OpenGWAS platform (https://gwas.mrcieu.ac.uk)

opengwas-api

Repository for the IEU epigenetics journal club papers, presentations and scripts

epigenetics-journal-club

Practicals for Genetic epidemiology short course

Lifecourse-GWAS

genetic-epidemiology-practicals

ukbb-prot-prs

gwas-vcf-performance

Comparison between VCF and plain text storage formats for GWAS summary statistics

Analysis code for proxy gene-by-environment Mendelian randomization of maternal smoking on offspring health

MR-maternal-smoking

ukbb-covid-collider

TeX

MR-randomization-test

Psychiatric-disorder-pheWAS-UKBB

ewascatalog-r

varGWAS

GWAS of trait variance (C++)

Smoking_IBD

Scripts for analysing the association between smoking and inflammatory bowel disease (IBD)

epigraphdb-ctda

codes for the epigraphdb CTAD database

education_mentalhealth_CVD

GwasDataImport

R package to upload data to GWAS database

biorxiv-medrxiv-tdm

ewascatalog

An MR-PheWAS of insomnia using UK Biobank and PHESANT.

PHESANT-MR-PheWAS-Insomnia

mendelvar_standalone

Standalone version of the MendelVar pipeline

R packages for mrcieu.r-universe.dev

mrcieu.r-universe.dev

sleep_duration_pregnancy

Here we provide scripts used in 'Investigating causal relations between sleep duration and risks of adverse pregnancy and perinatal outcomes: Linear and nonlinear Mendelian randomization analyses in up to 356,069 European women'

opengwas-requests

A place to request or contribute data to the IEU GWAS database

hie-ml

vitD_bonehealth

ALSPAC vitamin D and bone health MR study

PHESANT-MR-pheWAS-smoking

MR-pheWAS of smoking heaviness

met-d-import

UKBB Nightingale import to OpenGWAS

queryukbppp

Query UKB-PPP data

Schizophrenia_Fertility_Paper

Stata

handedness-ewas

epigraphdb_web

Web application (web UI) of the EpiGraphDB platform

Vue

gwas_processing

Docker container for creating indexes and indexing GWAS data

IGD-elasticsearch

Repository for the MR-PREG collaboration

variance-iv4-violation

varGWAS-ukbb-biomarkers

vcf-reference-datasets

Shell

MR-PREG

PHESANT-IV-pheWAS-relative-school-age

IV-pheWAS of relative school age

opengwas-infpval-fix

Documentation and fixes for p-value issues for some datasets

R package to perform regression-based Brown-Forsythe test

godmc_phase1_analysis

Shell

varGWASR

activityBigrams

Physical activity phenotyping with activity bigrams, and their association with BMI

MATLAB

COVIDITY_selbias

COVIDITY BHF-Project - Working Package 3 about selection bias in COVID-19 studies across UK cohorts

met-e-import

prot-c-import

Import Suhre et al 2017 protein data

opengwas

bbj-a-import

Import Japan Biobank GWAS

epigraphdb-asq

Annotated Semantic Queries

FinnGen R2 GWAS data import

mrtwin_power

cistrans_pqtl

finn-a-import

MVMRalcsmo

A repository of code for a MVMR study of the effect of alcohol and smoking on lung function

IlluminaFinalRep_LRRBAF

Estimate LRR and BAF from Illumina Final Report

Protein associations with lung cancer pre

prot-lungcancer

opengwas-reports

Report module for IEU GWAS pipeline

aries

Functions for loading the ARIES DNA methhylation data

Use upptime to monitor web platform status

upptime

JSON

finn-b-import

Import Finngen R5 GWAS

panukbb_gwas_import

Import pan UKBB GWAS analysis https://pan.ukbb.broadinstitute.org/

gwas2vcfweb

Web interface for gwas2vcf