Discover MRCIEU/GeneHackman 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-r

R package for epigraphdb

epigraphdb

Examples on using EpiGraphDB

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

gwas-vcf-specification

metaboprep

a pipeline of metabolomics data processing and quality control

PhenoSpD

gwasglue2

Connecting GWAS summary data to analytical tools

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

Binaries for tools used in genetics in an R package

genetics.binaRies

vectology

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

CheckSumStats

BiobankPhenotypes

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

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

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

finn-a-import

FinnGen R2 GWAS data import

mrtwin_power

opengwas

bbj-a-import

Import Japan Biobank GWAS

epigraphdb-asq

Annotated Semantic Queries

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

cistrans_pqtl

MVMRalcsmo

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