University of Bristol

Welcome to MRC Integrative Epidemiology Unit GitHub pages.

The MRC Integrative Epidemiology Unit at the University of Bristol (IEU) conducts some of the UK’s most advanced population health science research. It uses genetics, population data and experimental interventions to look for the underlying causes of chronic disease.

Researchers at the MRC IEU have created a range of openly available software tools based on research methods developed within the unit.

wordcloud

MRC IEU software browser

BESIDEMR R package

Bayesian model averaging approach to two-sample MR

bpbounds R package

nonparametric bounds for the ACE due to Balke and Pearl, JASA, 1997

bpbounds Stata package

Balke-Pearl nonparametric bounds for the average causal effect

cofunnel Stata package

contour enhanced funnel plots for meta-analysis

DataWatch

Smartwatch app for data capture using micro-ecological momentary assessment

dmrff

An R package for identifying differentially methylated regions in genome-wide DNA methylation profiles generated using the Illumina Beadchips or RRBS.

dnamalci

dnamalci is an R-package that provides functions to easily apply the DNA methylation alcohol scores (DNAm-Alcs) generated and characterized in: Liu C, Marioni RE, Hedman ÅK, Pfeiffer L, Tsai P-C, Reynolds LM et al. A DNA methylation biomarker of alcohol consumption. Mol Psychiatry 2016. doi:10.1038/mp.2016.192. Yousefi PD, Richmond R, Langdon R, Ness A, Liu C, Levy D et al. Validation and characterization of a DNA methylation alcohol biomarker across the life course. bioRxiv 2019. doi:10.1101/591404.

EpiGraphDB

A graph database and data mining platform for health data science

EpiGraphDB API

API of the EpiGraphDB platform

EpiGraphDB Graph Database

Neo4j graph database of the EpiGraphDB platform

EpiGraphDB R package

R package for EpiGraphDB

EpiGraphDB WebUI

EpiGraphDB platform web application

epigraphdbpy

Python package for EpiGraphDB

EpiViz

R package and shiny web app for the production of circos plots to display results from large epidemiological analyses

ewaff

R package for performing epigenome-wide association studies (EWAS).

The EWAS Catalog

A database of associations from EWAS summary datasets, for querying or download.

The EWAS Catalog R package

R package that can be used to query The EWAS Catalog database

The EWAS Catalog web app

The EWAS Catalog platform web application

FATHMM

Predicting the Functional Consequences of Non-Coding and Coding Single Nucleotide Variants (SNVs). Various different prediction algorithms, including FATHMM, FATHMM-MKL, FATHMM-XF, CScape

geograbi

A tool for efficiently grabbing usable metadata and experiment data off GEO for use in R.

GLU R package

A tool for analysing continuously measured glucose in epidemiology

gwas2vcf

Converts GWAS summary statistics into GWAS-VCF format

IEU GitHub Pages

Website promoting software developed by IEU members

ieugwaspy

Python package to access the IEU OpenGWAS API (modeled on ieugwasr)

iPVs

iPVs, identification of principal variables: The iPVs R package is designed to aid users with with the identification of representative (or independent) principal variables in an inter-correlated data set and to provide an estimation of the number of "independent" features (Me) to aid in deriving an appropriate Bonferroni corrected p-value for a study.

ivonesamplemr Stata package

Useful functions for one-sample (individual level data) Mendelian randomization and instrumental variable analyses

medrxivr

The goal of the medrxivr R package is two-fold. In the first instance, it provides programmatic access to the Cold Spring Harbour Laboratory (CSHL) API, allowing users to easily download medRxiv and bioRxiv preprint metadata (e.g. title, abstract, publication date, author list, etc) into R. The package also provides access to a maintained static snapshot of the medRxiv repository (see Data sources). Secondly, medrxivr provides functions to search the downloaded preprint records using regular expressions and Boolean logic, as well as helper functions that allow users to export their search results to a .BIB file for easy import to a reference manager and to download the full-text PDFs of preprints matching their search criteria.

meffil

R package providing functions for efficiently preprocessing and analyzing very large DNA methylation datasets generated using Infinium HumanMethylation450 or MethylationEPIC BeadChips.

MELODI

MELODI is a hypothesis generator. It identifies enriched overlapping objects which have been assigned to scientific literature and uses these to derive intermediate mechanisms.

MELODI-Presto

A quicker and more agile method to identify overlapping elements between any number of exposures and outcomes.

MendelVar

gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes

MetaboQC

A standardized pipeline for processing, QCing, and summarizing (un)targeted metabolomics data, with special considerations for data derived from the Nightingale and Metabolon platform.

Mood Music

A Django application to run an ecological momentary assessment study using text messaging through Twilio, and regularly collect API data (in this case Spotify, but generally adaptable). Currently in development, and may eventually be adapted as an reusable Django app.

mrbayes R package

Bayesian implementation of IVW and MR-Egger

mrdags R package

Code to draw DAG figures for MR studies

MR Dictionary

The MR Dictionary aims to provide useful definitions and descriptions for undertaking, understanding and interpreting MR studies to a wide, inter-disciplinary audience – both those new to MR and those who are experienced in its use but who want to remain up to date.

mrrobust Stata package

Stata version of MR methods

MVMR R package

Multivariable MR

NeDec

Causal network deconvolution

Neo4j Build Pipeline

Building a Neo4j graph using Snakemake and Docker

OneSampleMR R package

Useful functions for one-sample (individual level data) Mendelian randomization and instrumental variable analyses

OpenGWAS

A database of genetic associations from GWAS summary datasets, for querying or download.

OpenGWAS Elasticsearch Cluster

Terraform code to create OpenGWAS Elasticsearch cluster on Oracle Cloud

OpenGWAS Elasticsearch Indexer

Python code to add data to OpenGWAS Elasticsearch

PharmIV

a power calculator for instrumental variable analysis in pharmacoepidemiology

PHESANT R package

Run a phenome scan (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank

pygwasvcf

Python parser for GWAS-VCF

RadialMR R package

Radial MR

RbG Study Planner

RbG study planner assists in the planning stages and power assessment of recall by genotype studies.

reffadjust Stata package

random effects adjustment

RMVMR R package

Multivariable Radial MR

robvis

robvis makes it easy to produce high quality figures that summarise the risk-of-bias assessments performed as part of a systematic review or research synthesis project.

StopWatch

Smartwatch app for passive detection of cigarette smoking

TeMMPo

Text Mining for Mechanism Prioritization

Vectology

Exploring biomedical variable relationships using sentence embedding and vectors

xtmixediou Stata package

Stata command to estimate the linear mixed effects integrated Ornstein-Uhlenbeck model