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.
Bayesian model averaging approach to two-sample MR
nonparametric bounds for the ACE due to Balke and Pearl, JASA, 1997
Balke-Pearl nonparametric bounds for the average causal effect
contour enhanced funnel plots for meta-analysis
Smartwatch app for data capture using micro-ecological momentary assessment
An R package for identifying differentially methylated regions in genome-wide DNA methylation profiles generated using the Illumina Beadchips or RRBS.
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.
A graph database and data mining platform for health data science
API of the EpiGraphDB platform
Natural language query interface to the EpiGraphDB platform
Neo4j graph database of the EpiGraphDB platform
R package for EpiGraphDB
EpiGraphDB platform web application
Python package for EpiGraphDB
R package and shiny web app for the production of circos plots to display results from large epidemiological analyses
R package for performing epigenome-wide association studies (EWAS).
A database of associations from EWAS summary datasets, for querying or download.
R package that can be used to query The EWAS Catalog database
The EWAS Catalog platform web application
Predicting the Functional Consequences of Non-Coding and Coding Single Nucleotide Variants (SNVs). Various different prediction algorithms, including FATHMM, FATHMM-MKL, FATHMM-XF, CScape
A tool for efficiently grabbing usable metadata and experiment data off GEO for use in R.
A tool for analysing continuously measured glucose in epidemiology
Converts GWAS summary statistics into GWAS-VCF format
Website promoting software developed by IEU members
Wiki and knowledge base for IEU members
Python package to access the IEU OpenGWAS API (modeled on ieugwasr)
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.
Useful functions for one-sample (individual level data) Mendelian randomization and instrumental variable analyses
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.
R package providing functions for efficiently preprocessing and analyzing very large DNA methylation datasets generated using Infinium HumanMethylation450 or MethylationEPIC BeadChips.
MELODI is a hypothesis generator. It identifies enriched overlapping objects which have been assigned to scientific literature and uses these to derive intermediate mechanisms.
A quicker and more agile method to identify overlapping elements between any number of exposures and outcomes.
gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes
A standardized pipeline for processing, QCing, and summarizing (un)targeted metabolomics data, with special considerations for data derived from the Nightingale and Metabolon platform.
A Decision-Making System For Multiple Imputation. The Multiple Imputation DOCtor (midoc) R package is a decision-making system which incorporates expert, up-to-date guidance to help you choose the most appropriate analysis method when there are missing data. midoc will guide you through your analysis, examining the structure of the dataset to advise on whether multiple imputation (MI) is needed, and if so how to perform it.
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.
Bayesian implementation of IVW and MR-Egger
Code to draw DAG figures for MR studies
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.
Stata version of MR methods
Multivariable MR
Causal network deconvolution
Building a Neo4j graph using Snakemake and Docker
Useful functions for one-sample (individual level data) Mendelian randomization and instrumental variable analyses
A database of genetic associations from GWAS summary datasets, for querying or download.
Backend Python REST-API for https://gwas-api.mrcieu.ac.uk
Terraform code to create OpenGWAS Elasticsearch cluster on Oracle Cloud
Python code to add data to OpenGWAS Elasticsearch
a power calculator for instrumental variable analysis in pharmacoepidemiology
Run a phenome scan (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank
Python parser for GWAS-VCF
Radial MR
RbG study planner assists in the planning stages and power assessment of recall by genotype studies.
random effects adjustment
Multivariable Radial MR
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.
Smartwatch app for passive detection of cigarette smoking
Text Mining for Mechanism Prioritization
Sensitivity analysis using the trimmed means (TM) estimator: The tmsens R package is designed to aid users in performing a trimmed means analysis on a given dataset, and calculating, under assumption of normally distributed outcomes, the bias and bias-adjusted estimate for various user-specified parameters.
Software to perform GWAS of trait variance effects to prioritise loci for detection of genetic interaction effects
Exploring biomedical variable relationships using sentence embedding and vectors
Stata command to estimate the linear mixed effects integrated Ornstein-Uhlenbeck model