MRCIEU/TwoSampleMR

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Created almost 9 years ago
Updated 3 months ago

MRCIEU/TwoSampleMR

MRCIEU

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R package for performing 2-sample MR using MR-Base database

Mendelian randomization with GWAS summary data

A package for performing Mendelian randomization using GWAS summary data. It uses the IEU GWAS database to obtain data automatically, and a wide range of methods to run the analysis. You can use the MR-Base web app to try out a limited range of the functionality in this package, but for any serious work we strongly recommend using this R package.

January 2020 major update

We have made substantial changes to the package, database and reference panels. For full details of the changes, please visit https://mrcieu.github.io/TwoSampleMR/articles/gwas2020.html

Installation

To install the latest version of TwoSampleMR, perform as normal:

install.packages("remotes")
remotes::install_github("MRCIEU/TwoSampleMR")

To update the package just run the remotes::install_github("MRCIEU/TwoSampleMR") command again.

We recommend using this new version going forwards but for a limited time we are enabling backwards compatibility, in case you are in the middle of analysis or need to reproduce old analysis. In order to use the legacy version of the package and the database, install using:

install.packages("remotes")
remotes::install_github("MRCIEU/[email protected]")

Docker

A docker image containing R with the TwoSampleMR package pre-installed is available here: https://hub.docker.com/r/mrcieu/twosamplemr

Full documentation available here: https://mrcieu.github.io/TwoSampleMR

PHESANT

PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank

gwasglue

Linking GWAS data to analytical tools in R

ieugwasr

R interface to the IEU GWAS database API

gwasvcf

Reading, querying and writing GWAS summary data in VCF format

awesome-ai

Awesome list for all things AI, ML and deep learning

gwas2vcf

Convert GWAS summary statistics to VCF

MRInstruments

Data objects for various sets of instruments

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

Jupyter Notebook

epigraphdb-r

R package for epigraphdb

metaboprep

a pipeline of metabolomics data processing and quality control

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

Jupyter Notebook

UKBiobankGWAS

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

godmc

GoDMC analysis pipeline

PHESANT-MR-pheWAS-BMI

GLU

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

ieugwaspy

Python interface to the MRC IEU GWAS database API

GeneHackman

Pipeline for genetic epidemiology projects at Univsersity of Bristol

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

Jupyter Notebook

CheckSumStats

BiobankPhenotypes

pygwasvcf

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

melodi

Mining Enriched Literature Objects to Derive Intermediates

ariesmqtl

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

bp-drug-mr

Multi-ancestry MR of blood pressure drug targets

temmpo

Text mining for mechanism prioritisation

godmc_phase2_analysis

qqman_multiple_colours

Manhattan plot function which highlights SNPs in different 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

opengwas-api

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

epigenetics-journal-club

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

Lifecourse-GWAS

genetic-epidemiology-practicals

Practicals for Genetic epidemiology short course

ukbb-prot-prs

gwas-vcf-performance

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

MR-maternal-smoking

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

ukbb-covid-collider

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

Jupyter Notebook

ewascatalog

PHESANT-MR-PheWAS-Insomnia

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

mendelvar_standalone

Standalone version of the MendelVar pipeline

mrcieu.r-universe.dev

R packages for 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

handedness-ewas

epigraphdb_web

Web application (web UI) of the EpiGraphDB platform

gwas_processing

IGD-elasticsearch

Docker container for creating indexes and indexing GWAS data

variance-iv4-violation

varGWAS-ukbb-biomarkers

vcf-reference-datasets

MR-PREG

Repository for the MR-PREG collaboration

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

godmc_phase1_analysis

varGWASR

R package to perform regression-based Brown-Forsythe test

activityBigrams

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

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

Jupyter Notebook

mrtwin_power

cistrans_pqtl

finn-a-import

FinnGen R2 GWAS data 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

prot-lungcancer

Protein associations with lung cancer pre

opengwas-reports

Report module for IEU GWAS pipeline

aries

Functions for loading the ARIES DNA methhylation data

upptime

Use upptime to monitor web platform status

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

mrmn

Website for the Mendelian randomization Methods Network

AFS_AAM_LifeHistory

Analysis scripts for "Using Mendelian randomization to investigate life history theory: the effects of age at menarche and first sexual intercourse on reproductive and behavioural outcomes"

oci-elastic

IEU version of https://github.com/cloud-partners/oci-elastic

mdNLR-and-Rheumatoid-Arthritis-Script

Rheumatoid arthritis (RA) is a disease of chronic systemic inflammation (SI). In the present study, we used four datasets to explore whether methylation-derived neutrophil-to-lymphocyte ratio (mdNLR) might be a marker of SI in new onset, untreated, and treated prevalent RA cases and/or a marker of treatment response to the tumour necrosis factor inhibitor (TNFi) etanercept.