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TwoSampleMR - Two Sample MR Functions and Interface to MRC Integrative Epidemiology Unit OpenGWAS Database

A package for performing Mendelian randomization using GWAS summary data. It uses the IEU OpenGWAS database <https://opengwas.io> to automatically obtain data, and a wide range of methods to run the analysis.

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11.83 score 548 stars 2 dependents 2.2k scripts

ieugwasr - Interface to the 'OpenGWAS' Database API

Interface to the 'OpenGWAS' database API <https://api.opengwas.io/api/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.

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11.37 score 109 stars 7 dependents 740 scripts 3.8k downloads

pcaMethods - A collection of PCA methods

Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.

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bayesianlooking-for-maintainercpp

11.08 score 55 stars 78 dependents 688 scripts

gwasrapidd - 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

'GWAS' R 'API' Data Download. This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by accessing the 'REST' 'API' <https://www.ebi.ac.uk/gwas/rest/docs/api/>.

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thirdpartyclientbiomedicalinformaticsgenomewideassociationsnpassociation-studiesgwas-cataloghumanrest-clienttraittrait-ontology

8.37 score 103 stars 1 dependents 85 scripts 839 downloads

MVMR - MVMR

An R package for performing multivariable Mendelian randomization analyses.

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8.12 score 54 stars 1 dependents 210 scripts

GenomicSEM - Structural equation modeling based on GWAS summary statistics

Later

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7.60 score 278 stars 182 scripts

MendelianRandomization - Mendelian Randomization Package

Encodes several methods for performing Mendelian randomization analyses with summarized data. Summarized data on genetic associations with the exposure and with the outcome can be obtained from large consortia. These data can be used for obtaining causal estimates using instrumental variable methods.

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openblascpp

7.43 score 45 stars 1 dependents 788 scripts 2.5k downloads

OneSampleMR - One Sample Mendelian Randomization and Instrumental Variable Analyses

Useful functions for one-sample (individual level data) Mendelian randomization and instrumental variable analyses. The package includes implementations of; the Sanderson and Windmeijer (2016) <doi:10.1016/j.jeconom.2015.06.004> conditional F-statistic, the multiplicative structural mean model Hernán and Robins (2006) <doi:10.1097/01.ede.0000222409.00878.37>, and two-stage predictor substitution and two-stage residual inclusion estimators explained by Terza et al. (2008) <doi:10.1016/j.jhealeco.2007.09.009>.

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instrumental-variableinstrumental-variablesmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomization

7.31 score 25 stars 34 scripts 239 downloads

metaboprep - Metabolomics data preparation and processing pipeline

| Reads in raw Metabolon, Nightingale Health, Olink, and SomaLogic xls sheets, or flat text files and aids in data preparation of all metabolomics & proteomics data sets.

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7.30 score 27 stars 23 scripts

gwasvcf - Tools for Dealing with GWAS Summary Data in VCF Format

Tools for dealing with GWAS summary data in VCF format. Includes reading, querying, writing, as well as helper functions such as LD proxy searches.

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7.20 score 105 stars 166 scripts

rsnps - Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web

A programmatic interface to various 'SNP' 'datasets' on the web: 'OpenSNP' (<https://opensnp.org>), and 'NBCIs' 'dbSNP' database (<https://www.ncbi.nlm.nih.gov/projects/SNP/>). Functions are included for searching for 'NCBI'. For 'OpenSNP', functions are included for getting 'SNPs', and data for 'genotypes', 'phenotypes', annotations, and bulk downloads of data by user.

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genesnpsequenceapiwebapi-clientspeciesdbsnpopensnpncbigenotypedatasnpsweb-api

7.17 score 55 stars 1 dependents 74 scripts 54 downloads

causl - Methods for Specifying, Simulating from and Fitting Causal Models

Model and simulate from multivariate distributions using marginal causal parameters.

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openblascppopenmp

7.10 score 22 stars 65 scripts

RadialMR - RadialMR

A package for implementing radial inverse variance weighted and MR-Egger methods.

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6.53 score 35 stars 4 dependents 147 scripts

midoc - A Decision-Making System for Multiple Imputation

A guidance system for analysis with missing data. It incorporates expert, up-to-date methodology to help researchers choose the most appropriate analysis approach when some data are missing. You provide the available data and the assumed causal structure, including the likely causes of missing data. 'midoc' will advise which analysis approaches can be used, and how best to perform them. 'midoc' follows the framework for the treatment and reporting of missing data in observational studies (TARMOS). Lee et al (2021). <doi:10.1016/j.jclinepi.2021.01.008>.

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missing-datamultiple-imputation

6.51 score 8 stars 20 scripts 208 downloads

MRPRESSO - Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) test.

MR-PRESSO (Mendelian Randomization Pleiotropy RESidual Sum and Outlier) is a framework that allows for the evaluation of pleiotropy in multi-instrument Mendelian Randomization utilizing genome-wide summary association statistics.

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6.26 score 95 stars 3 dependents 429 scripts

epigraphdb - Interface Package for the 'EpiGraphDB' Platform

The interface package to access data from the 'EpiGraphDB' <https://epigraphdb.org> platform. It provides easy access to the 'EpiGraphDB' platform with functions that query the corresponding REST endpoints on the API <https://api.epigraphdb.org> and return the response data in the 'tibble' data frame format.

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api-clientbioinformaticsepidemiologygraph-databasemendelian-randomizationphenotypes

6.16 score 30 stars 16 scripts 308 downloads

robvis - Visualize the Results of Risk-of-Bias (ROB) Assessments

Helps users in quickly visualizing risk-of-bias assessments performed as part of a systematic review. It allows users to create weighted bar-plots of the distribution of risk-of-bias judgments within each bias domain, in addition to traffic-light plots of the specific domain-level judgments for each study. The resulting figures are of publication quality and are formatted according the risk-of-bias assessment tool use to perform the assessments. Currently, the supported tools are ROB2.0 (for randomized controlled trials; Sterne et al (2019) <doi:10.1136/bmj.l4898>), ROBINS-I (for non-randomised studies of interventions; Sterne (2016) <doi:10.1136/bmj.i4919>), and Quality & Applicability of Diagnostic Accuracy Studies V2 (Whiting et al (2011) <doi:10.7326/0003-4819-155-8-201110180-00009>), and QUIPS (Hayden et al (2013) <doi:10.7326/0003-4819-158-4-201302190-00009>.

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6.14 score 1 stars 102 scripts 6.7k downloads

omiprep - Omics data preparation and processing pipeline

| Reads in raw Metabolon, Nightingale Health, Olink, and SomaLogic xls sheets, or flat text files and aids in data preparation of all metabolomics & proteomics data sets. Formerly known as metaboprep.

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5.94 score 16 scripts

mrbayes - Bayesian Summary Data Models for Mendelian Randomization Studies

Bayesian estimation of inverse variance weighted (IVW), Burgess et al. (2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden et al. (2015) <doi:10.1093/ije/dyv080>, summary data models for Mendelian randomization analyses.

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cpp

5.72 score 4 stars 9 scripts 277 downloads

gpmapr - Query the OpenGWAS genotype-phenotype map

This package is a simple wrapper around the OpenGWAS genotype-phenotype map API.

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5.64 score 6 stars 10 scripts

genepi.utils - GenEpi Utility Functions

The genepi.utils package is a collection of utility functions for working with genetic epidemiology data.

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5.58 score 11 stars 14 scripts

gwasglue2 - GWAS summary data sources connected to analytical tools

Description: Many tools exist that use GWAS summary data for colocalisation, fine mapping, Mendelian randomization, visualisation, etc. This package is a conduit that connects R packages that can retrieve GWAS summary data to various tools for analysing those data.

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5.46 score 23 stars 1 dependents 12 scripts

mr.raps - Two Sample Mendelian Randomization using Robust Adjusted Profile Score

Mendelian randomization is a method of identifying and estimating a confounded causal effect using genetic instrumental variables. This packages implements methods for two-sample Mendelian randomization with summary statistics by using Robust Adjusted Profile Score (RAPS). References: Qingyuan Zhao, Jingshu Wang, Gibran Hemani, Jack Bowden, Dylan S. Small. Statistical inference in two-sample summary-data Mendelian randomization using robust adjusted profile score. <arXiv:1801.09652>; Qingyuan Zhao, Yang Chen, Jingshu Wang, Dylan S. Small. Powerful genome-wide design and robust statistical inference in two-sample summary-data Mendelian randomization. <arXiv:1804.07371>.

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5.35 score 42 stars 1 dependents 176 scripts 52 downloads

MRInstruments - Data sources for genetic instruments to be used in MR

Datasets of eQTLs, GWAS catalogs, etc.

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5.28 score 48 stars 266 scripts

hdi - High-Dimensional Inference

Implementation of multiple approaches to perform inference in high-dimensional models.

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5.27 score 2 stars 5 dependents 244 scripts 5.1k downloads

GWASBrewer - Simulate Realistic GWAS Summary Statistics

Simulate GWAS summary statistics from specified DAG or factor structure.

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openblascpp

5.20 score 11 stars 24 scripts

gwasglue - GWAS summary data sources connected to analytical tools

Many tools exist that use GWAS summary data for colocalisation, fine mapping, Mendelian randomization, visualisation, etc. This package is a conduit that connects R packages that can retrieve GWAS summary data to various tools for analysing those data.

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5.17 score 141 scripts

alspac - Data dictionary for ALSPAC

Functions to search and extract variables based on keywords from the ALSPAC data dictionary.

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5.16 score 11 stars 47 scripts

genetics.binaRies - Binaries for Tools Used in Genetics in an R Package

A convenient way to make binaries such as plink, bcftools, and others available to other packages. This package forms part of the MRC IEU OpenGWAS system. The system includes other R packages, including; gwasglue, ieugwasr, gwasvcf, and TwoSampleMR.

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5.13 score 12 stars 1 dependents 75 scripts

CAMeRa - CAMeRa (Cross Ancestral Mendelian Randomisation)

CAMERA estimates joint causal effect in multiple ancestries and detects pleiotropy via the zero relevance model.

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causal-inferencegwas-summary-statisticsmendelian-randomisationmulti-ancestry

5.12 score 3 stars 222 scripts

GwasDataImport - Import EBI Data to OpenGWAS

Determine the new EBI data not present in OpenGWAS. Download dataset and import metadata. Upload processed data and metadata to OpenGWAS.

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5.05 score 3 stars 18 scripts

MRMix - Mendelian Randomization Analysis Using Mixture Models (MRMix)

This package gives robust estimation of causal effects by conducting Mendelian randomization analysis using a mixture model approach.

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5.04 score 25 stars 3 dependents 97 scripts

triangulate - Useful functions for performing evidence triangulation

What the package does (one paragraph).

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5.03 score 4 stars 10 scripts

EpiViz - EpiViz

An implementation of Circos plots for epidemiologists in R. It takes the Circlize package and adapts it for use by epidemiologists. Circos plots provide an informative way of plotting greater than 50 plotting points. A legend can be plotted automatically and customised.

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4.89 score 9 stars 43 scripts

bpbounds - Nonparametric Bounds for the Average Causal Effect Due to Balke and Pearl and Extensions

Implementation of the nonparametric bounds for the average causal effect under an instrumental variable model by Balke and Pearl (Bounds on Treatment Effects from Studies with Imperfect Compliance, JASA, 1997, 92, 439, 1171-1176, <doi:10.1080/01621459.1997.10474074>). The package can calculate bounds for a binary outcome, a binary treatment/phenotype, and an instrument with either 2 or 3 categories. The package implements bounds for situations where these 3 variables are measured in the same dataset (trivariate data) or where the outcome and instrument are measured in one study and the treatment/phenotype and instrument are measured in another study (bivariate data).

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aceaverage-causal-effectboundsinstrumental-variableivmendelianmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomizationmrnonparametricnonparametric-boundspearlshiny

4.85 score 13 scripts 697 downloads

ivmodel - Statistical Inference and Sensitivity Analysis for Instrumental Variables Model

Carries out instrumental variable estimation of causal effects, including power analysis, sensitivity analysis, and diagnostics. See Kang, Jiang, Zhao, and Small (2021) <https://muse.jhu.edu/article/804372> for details.

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4.81 score 10 stars 129 scripts 514 downloads

nlmr - Non-linear Mendelian randomisation

Non-linear Mendelian randomization analysis to investigate the shape of exposure-outcome relationships.

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4.78 score 56 stars 213 scripts

cause - CAUSE: Causal Analysis Using Summary Effect Estimates

Identify causal patterns using pairs of GWAS summary statistics.

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cpp

4.54 score 59 stars 118 scripts

geni.plots - GENI plots

GENI plots is designed to visualise results from genome-wide association studies.

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4.51 score 32 stars 20 scripts

simmrd - Simulation of Mendelian Randomization data

This package generates simulation data to use in the evaluation of univariable or multivariable Mendelian Randomization methods. MR scenarios can include uncorrelated horizontal pleiotropy, correlated horizontal pleiotropy, weak instruments, winner's curse, and correlated SNP instruments.

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4.10 score 5 stars 5 scripts

MRPC - PC Algorithm with the Principle of Mendelian Randomization

A PC Algorithm with the Principle of Mendelian Randomization. This package implements the MRPC (PC with the principle of Mendelian randomization) algorithm to infer causal graphs. It also contains functions to simulate data under a certain topology, to visualize a graph in different ways, and to compare graphs and quantify the differences. See Badsha and Fu (2019) <doi:10.3389/fgene.2019.00460>, Badsha, Martin and Fu (2021) <doi:10.3389/fgene.2021.651812>, Kvamme and Badsha, et al. (2025) <doi:10.1093/genetics/iyaf064>.

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4.10 score 8 stars 26 scripts 679 downloads

RMVMR - RMVMR

An R package for performing radial multivariable Mendelian randomization analyses.

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4.03 score 13 stars 15 scripts

gsmr2 - gsmr2 - a tool for causal inference between complex traits

GSMR2 (Generalised Summary-data-based Mendelian Randomisation v2) is an improved version of GSMR, which uses GWAS summary statistics to test for a putative causal association between two phenotypes (e.g., a modifiable risk factor and a disease) based on a multi-SNP model. This version implements a global heterogeneity test to remove invalid instrumental variables and provides a causal estimation that is more robust to directional pleiotropy.

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4.02 score 21 stars 5 scripts

SUMnlmr - Non-Linear Mendelian Randomization On Partially Summarized Data

Runs non-linear MR calculations on partly-summarized data.

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3.97 score 22 stars 21 scripts

MRAPSS - The MRAPSS package implement the MR-APPSS approach to test for the causal effect of an exposure on a outcome disease.

The MRAPSS package implement the MR-APPSS approach to test for the causal effects between an exposure and a outcome disease. The MR-APPSS is a unified approach to Mendelian Randomization accounting for polygenicity, pleiotropy and sample structure using genome-wide summary statistics. Specifically, MR-APPSS uses a background-foreground model to characterize both SNP-exposure effects and SNP-outcome effects estimates, where the background model accounts for confounding from genetic correlation and sample structure and the foreground model captures the valid signal for causal inference.

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3.89 score 43 stars 36 scripts

cit - Causal Inference Test

A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. Described in Millstein, Chen, and Breton (2016), <DOI:10.1093/bioinformatics/btw135>, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.

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gslcpp

3.88 score 2 stars 38 scripts 271 downloads

mrSampleOverlap - Estimate Bias Due To Sample Overlap In Mendelian Randomization Studies

A function to estimate bias due to sample overlap in Mendelian Randomization studies.

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3.78 score 12 stars 5 scripts

aciccomp2016 - Atlantic Causal Inference Conference Competition 2016 Simulation

Generate simulation data.

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3.75 score 45 stars 25 scripts

gsmr - gsmr - a tool for SMR and HEIDI analysis

A tool perform Generalized Summary-data-based Mendelian Randomization analysis (GSMR) and HEterogeneity In Dependent Instruments analysis to remove pleiotropic outliers (HEIDI-outlier)

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3.71 score 3 stars 34 scripts

mrsensemakr - Sensitivity Analysis Tools for Mendelian Randomization

Implements sensitivity analysis tools for Mendelian Randomization, as discussed in Cinelli et al. (2020) <doi:10.1101/2020.10.21.347773>. Provides functions for computing sensitivity statistics, robustness values, and bias-adjusted estimates for instrumental variable analyses, along with sensitivity contour plots for visualizing the impact of potential violations of the exclusion restriction.

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3.70 score 10 stars 6 scripts

MRBEE - Mendelian Randomization using Bias-Corrected Estimating Equation and Iterative Pleiotropy Testing

This package performs multivariate Mendelian randomization. It is characterized by the removal of measurement error bias caused by the estimation error of GWAS effect size estimates using an unbiased estimating function in measurement error analysis. It also utilizes a pleiotropy test to dynamically detect and remove potential pleiotropy, making the causal effect robust to pleiotropy.

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3.61 score 9 stars 15 scripts

MRcML - Mendelian randomization method with constrained maximum likelihood.

Perform MRcML method.

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3.59 score 15 stars 52 scripts

lhcMR - Latent Heritable Confounder - Mendelian Randomisation

lhcMR esimates a causal effect between two traits while accounting for a possible latent heritable confounder acting on them, as well as sample overlap.

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3.55 score 26 stars 27 scripts

DRMR - Doubly-Ranked Stratification in Mendelian Randomization

Doubly-ranked and residual stratification for instrumental variable and Mendelian randomization studies and further stratification-based analysis.

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3.54 score 11 stars 21 scripts

prop.coloc - A frequentist test of proportional colocalization after selecting relevant genetic variants

A proportional colocalization test that accounts for uncertainty in variant selection using summary data.

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3.40 score 5 stars 2 scripts

MR.RGM - Fitting Multivariate Bidirectional Mendelian Randomization Networks Using Bayesian Directed Cyclic Graphical Models

Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. The resulting Graph visually represents these causal connections, showing directed edges with effect sizes labeled. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. The method also optionally incorporates measured covariates (when available) and allows flexible modeling of the error variance structure, including correlated errors that may reflect unmeasured confounding among responses. In the process, causal effects, adjacency matrices, and other essential parameters of the complex biological networks, are estimated. Besides, 'MR.RGM' provides uncertainty quantification for specific network structures among response variables. Parts of the Inverse Wishart sampler are adapted from the econ722 repository by DiTraglia (GPL-2.0).

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openblascppopenmp

3.38 score 1 stars 12 scripts 192 downloads

BWMR - Bayesian Weighted Mendelian Randomization (BWMR)

Inference the causality based on BWMR method.

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3.32 score 42 scripts

MRCorge - Mendelian Randomization based on the core gene hypothesis for polygenic exposures

This package performs Mendelian Randomization (MR) analyses based on the core gene hypothesis for polygenic exposures. MR CORGE identifies a small number of putative core instruments that are more likely to affect genes with a direct biological role in an exposure and obtains causal effect estimates based on these instruments, thereby reducing the risk of horizontal pleiotropy.

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3.30 score 4 stars 6 scripts

navmix - A package for performing directional clustering by fitting a noise-augmented von Mises-Fisher mixture model

A package for performing directional clustering by fitting a noise-augmented von Mises-Fisher mixture model

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3.30 score 4 stars 4 scripts

PPMR - Probabilistic Two Sample Mendelian Randomization

Efficient statistical inference of two-sample MR (Mendelian Randomization) analysis. It can account for the correlated instruments and the horizontal pleiotropy, and can provide the accurate estimates of both causal effect and horizontal pleiotropy effect as well as the two corresponding p-values. There are two main functions in the 'PPMR' package. One is PMR_individual() for individual level data, the other is PMR_summary() for summary data.

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openblascppopenmp

3.30 score 2 stars 20 scripts 186 downloads

FLOWMR - An R Package for Mendelian Randomization in the mediation setting

A Bayesian framework for Mendelian Randomization in the mediation setting.

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openblascppopenmp

3.26 score 18 stars 4 scripts

proxysnps - Get proxy SNPs for a SNP in the 1000 Genomes Project

This package implements functions to query remote VCF files. You can use it to find proxy SNPs in linkage disequilibrium with SNPs of interest or to calculate allele frequencies in different populations.

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bioinformaticslinkage-disequilibriumsnpsstatistics

3.19 score 31 stars 8 scripts

mrclust - Identifying Clustered Heterogeneity in Mendelian Randomization Analyses

Performs likelihood based clustering on univariate observations with known uncertainty (via standard error data), whilst accounting for possible null and junk components in the sample.

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3.16 score 18 stars 16 scripts

CheckSumStats - CheckSumStats

CheckSumStats is an R package for checking the accuracy of meta- and summary-data from genome-wide association studies (GWAS) prior to their use in post-GWAS applications. For example, the package provides tools for checking that the reported effect allele and effect allele frequency columns are correct. It also checks for possible issues in the reported effect sizes that might introduce bias into downstream analyses.

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3.11 score 10 stars 26 scripts

mrpipeline - Implements a Ready-for-Use Mendelian Randomisation Pipeline

This package implements a pipeline which in turns allows for simple and generally "hands-free" Mendelian randomisation analyses to be run. Data may be used from the OpenGWAS DB or locally, using .vcf files. Analyses include MR, colocalisation and standard MR sensitivity analyses. Please see the documentation for more details.

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3.07 score 6 stars 39 scripts

mrbma - Mendelian Randomization Bayesian Model Averaging

A set of functions designed to implement Mendelian Randomization Bayesian Model Averaging.

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3.06 score 23 stars 2 scripts

MR2 - Bayesian multi-response Mendelian randomisation

This package performs two-sample summary-level data Bayesian multi-response Mendelian randomisation with the selection of important exposures shared or distinct across responses. Post-processing and selection of exposures based on an in-house FDR implementation are also provided.

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3.02 score 21 stars

MRTool - Simulating Data for Mendelian Randomization Scenarios Based on Genotype Data

This package can be used to simulate data in R for Mendelian Randomization scenarios including confounder, exposure and outcome. Recommended MR package is MendelianRandomization.

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3.00 score

varGWASR - Least Absolute Deviation Regression Brown Forsythe Test

Brown-Forsythe SNP test using LAD regression and variance effect estimate

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geneticsheteroscedasticityheteroskedasticitystatisticsvariance

3.00 score 2 stars

mr.simss - MR-SimSS: Mendelian Randomisation (MR) method that combats Winner's Curse using a simulated sample splitting approach

Designed to provide users with a method, namely MR-SimSS, which uses simulated sample splitting in order to alleviate Winner's Curse bias in MR causal effect estimates. This approach also takes into account sample overlap between the exposure and outcome genome-wide association studies. It uses summary statistics from genome-wide association studies and works in combination with existing MR methods, such as IVW and MR-RAPS.

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2.95 score 1 stars 6 scripts

MRAID - MRAID(Mendelian Randomization with Automated Instrument Determination)

MRAID is an R package for efficient statistical inference of two-sample Mendelian Randomization. MRAID takes GWAS summary statistics as inputs to estimate causal effects of one trait on another. MRAID is able to model an initial set of candidate SNP instruments that are in high LD with each other and perform automated instrument selection to identify suitable SNPs to serve as instrumental variables. MRAID simultaneously accounts for both uncorrelated and correlated horizontal pleiotropy, relies on a scalable sampling-based inference algorithm to perform numerical integration, circumventing the difficulty in likelihood function, leading to calibrated p-values that enable reasonably large-scale exposure screening.

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openblascpp

2.94 score 16 stars 11 scripts

screening - What the Package Does (one line, title case)

What the package does (one paragraph).

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2.81 score 13 stars 8 scripts

locuscomparer - locuscomparer: Visualization of GWAS-QTL Colocalization Events

locuscomparer is the standalone version of the LocusCompare webserver (www.locuscompare.ml:3838). locuscomparer performs visualization of colocalization of summary statistics from pairs of association datasets (e.g. GWAS and eQTL).

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2.80 score 125 scripts

mrlocus - MRLocus - Mendelian Randomization per locus

Mendelian Randomization per locus, leveraging eQTL and GWAS summary statistics, for estimation of gene-to-trait effect size and dispersion.

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cpp

2.74 score 1 stars 11 scripts

MVMRcML - Multivariable Mendelian randomization based on constrained maximum likelihood

Robust multivariable Mendelian randomization based on constrained maximum likelihood.

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openblascpp

2.74 score 11 stars 7 scripts

CIVMR - Constrained Instrumental Variables in Mendelian Randomization with Pleiotropy

In Mendelian randomization (MR), genetic variants are used to construct instrumental variables that then enable inference about the causal relationship between a phenotype of interest and a response or disease outcome. However, valid MR inference requires several assumptions, including the assumption that the genetic variants only influence the response through the phenotype of interest.Pleiotropy occurs when a genetic variant has an effect on more than one different phenotypes, and therefore a pleiotropic genetic variant may be an invalid instrumental variable.Hence, a naive method for constructing an instrumental variables may lead to biased estimation of the association between the phenotype and the response. Here, we encode a new and intuitive method (Constrained Instrumental Variable method [CIV]) to construct valid instrumental variables and perform adjusted causal effect estimation when pleiotropic exists, focusing particularly on the situation where pleiotropic phenotypes have been measured. Our approach is theoretically guaranteed to perform an automatic and valid selection of genetic variants when building the instrumental variable. We also provide details of the features of many existing methods, together with a comparison of their performance in a large series of simulations. CIV performs robustly across many different pleiotropic violations of the MR assumptions.

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2.70 score

MrDAG - MrDAG: Bayesian causal graphical model for joint Mendelian randomization analysis of multiple exposures and outcomes

This package performs Mendelian randomization for multiple exposures and outcomes with Bayesian structure learning and causal effects estimation. The directionality of the causal effects between the exposures and the outcomes is assumed known, i.e., the exposures can only be potential causes of the outcomes and no reverse causation is allowed.

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2.70 score 10 stars

tmsens - Sensitivity Analysis Using the Trimmed Means Estimator

Sensitivity analysis using the trimmed means estimator.

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missing-datasensitivity-analysistrimmed-means

2.70 score 1 stars 6 scripts 267 downloads

mr.pivw - Penalized Inverse-Variance Weighted Estimator for Mendelian Randomization

The penalized inverse-variance weighted (pIVW) estimator is a Mendelian randomization method for estimating the causal effect of an exposure variable on an outcome of interest based on summary-level GWAS data. The pIVW estimator accounts for weak instruments and balanced horizontal pleiotropy simultaneously. See Xu S., Wang P., Fung W.K. and Liu Z. (2022) <doi:10.1111/biom.13732>.

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2.70 score 1 scripts 117 downloads

tryx - MR-TRYX (treasure your exceptions)

Heterogeneity in MR analyses can arise due to horizontal pleiotropy. This package uses MR-Base to identify possible traits that can explain the heterogeneity, with a view to identifying novel putative associations, and adjusting for their influences to reduce heterogeneity and improve power.

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2.70 score 10 stars 9 scripts

gassocplot - Regional association plots

This package is used plot regional association plots.

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2.67 score 47 scripts

indexevent - Adjustment for index event bias

Adjusts association statistics for index event bias in the context of a genome-wide association study for a subsequent event.

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2.58 score 4 stars 19 scripts

finemapr - R wrapper to fine-mappers

R wrapper to fine-mappers.

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2.48 score 6 scripts

MVMRcMLSuSiE - Implementation of MVMR-cML-SuSiE

Implements the first three steps of constrained Maximum Likelihood (cML) based Mendelian randomization approach for highly correlated exposures

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2.48 score 6 stars 4 scripts

GraphMRcML - Causal Network Inference via Mendelian Randomization with cML and Network Deconvolution

Combines Mendelian randomization (constrained maximum likelihood, cML) and network deconvolution for inference of causal networks from GWAS summary data, as described in Lin, Xue, and Pan (2023) <doi:10.1371/journal.pgen.1010762>.

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2.43 score 9 stars

winnerscurse - Winner's Curse Adjustment Methods for Summary Statistics from Genome-Wide Association Studies

Designed to provide users with easy access to published methods which aim to correct for Winner's Curse using only summary statistics from genome-wide association studies. With merely estimates of effect size and associated standard error for each genetic variant, users are able to implement these methods to obtain more accurate estimates of the true effect sizes. These methods can be applied to data from both quantitative and binary traits.

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2.40 score 5 stars 4 scripts

BESIDEMR - BayEsian Set IDEntification Mendelian randomization

The R package to perform BayEsian Set IDEntification Mendelian randomization (BESIDE-MR).

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2.40 score 5 stars

FusioMR - Flexible, Unified and Versatile Mendelian Randomization

A Bayesian Mendelian Randomization framework for causal effect estimation from GWAS summary statistics. Supports single and multiple exposure/outcome analyses with optional correlated horizontal pleiotropy.

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openblascpp

2.30 score 2 stars 4 scripts

mr.divw - debiased inverse-variance weighted estimator for univariable and multivariable Mendelian randomization

Perform causal effect estimation for summary-data Mendelian randomization using IVW, dIVW and MV-SRIVW estimators.

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2.26 score 12 scripts

gassocplot2 - Regional association plots

This package is used plot regional association plots.

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2.26 score 18 scripts

TVMR - Time-varying Mendelian randomization with time-continous modelling for the effect function

Use functional principal components analysis (FPCA) within multivariable Mendelian randomization (MVMR) to estimate the time-varying effect function.

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2.18 score 3 stars 2 scripts

lmrse - Linear regression with clustered robust standard errors

Longtiudinal analysis of high-dimensional data using linear regression with clustered robust standard errors across markers.

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cpp

2.18 score 3 stars 1 scripts

GRAPPLE - R Package for MR Framework GRAPPLE

Fitting and diagnosing two-sample summary data Mendelian randomization with heterogeneous instruments.

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2.10 score 25 scripts

SlopeHunter - Slope-Hunter: A ROBUST METHOD FOR COLLIDER BIAS CORRECTION IN CONDITIONAL GENOME-WIDE ASSOCIATION STUDIES

Studying genetic associations with prognosis (e.g. survival, disability, subsequent disease events) is problematic due to selection bias - also termed index event bias or collider bias - whereby selection on disease status can induce associations between causes of incidence with prognosis. The Slope-Hunter approach adjusts genetic associations for this bias assuming that the contribution of the set of genetic variants affecting incidence only to the heritability of incidence is at least as large as the contribution of those affecting both incidence and prognosis.

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2.10 score 1 stars 25 scripts

MR.CUE - Mendelian randomization accounting for complex correlated horizontal pleiotropy while elucidating shared genetic etiology

Mendelian randomization accounting for complex correlated horizontal pleiotropy while elucidating shared genetic etiology.

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openblascppopenmp

2.04 score 11 scripts

RMR.ICP - Robust Mendelian Randomization method to account for Idiosyncratic and Correlated Pleiotropy

Robust Mendelian Randomization method to account for Idiosyncratic and Correlated Pleiotropy.

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openblascppopenmp

2.00 score 2 scripts

MVMR.CUE - Multivariable Mendelian randomization accounting for complex correlated horizontal pleiotropy while elucidating shared genetic etiology

Multivariable Mendelian randomization accounting for complex correlated horizontal pleiotropy while elucidating shared genetic etiology.

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openblascppjags

2.00 score 1 scripts

jlst - Joint location-and-scale tests

Joint location-and-scale tests for joint testing of mean (location) and variance (scale).

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2.00 score 2 stars 2 scripts

MRchecks - Tools for detecting genetic variants whose effect changes with age and associated bias

This package is a collection of tools to detect SNPs whose effect varies with age whose. owoeosds sd sd. sdsfw. sdfsers s es .

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2.00 score 2 stars

MR.LDP - What the Package Does Using Title Case

More details about what the package does. See <http://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file> for details on how to write this part.

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openblascppopenmp

1.90 score 1 stars 16 scripts

journalclub - Journal club papers

Uses citations and PubMed queries to generate new publications for a journal club.

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1.78 score 12 scripts

MR.Corr2 - MR.Corr2

More details about what the package does. See <http://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file> for details on how to write this part.

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openblascppopenmp

1.74 score 11 scripts

qbaconfound - Monte Carlo Quantitative Bias Analysis for Unmeasured Confounding

A flexible Monte Carlo quantitative bias analysis (QBA) for unmeasured confounding in observational studies, as described in Hughes et al. The substantive analysis may be a generalised linear model or a Cox proportional hazards model with a binary, continuous, or categorical exposure and measured confounders. The method allows for one or more binary or continuous unmeasured confounders that may be correlated with the measured confounders. Informative priors for a small number of bias parameters encode external information about the unmeasured confounders.

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1.70 score

RFQT - Random Forest of Q Trees

Data-adaptive method for effect heterogeneity analysis or non-linear causal studies in Mendelian randomization and instrumental variables analysis.

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1.70 score 1 scripts

mr.genius - GENIUS-MAWII: For Robust Mendelian Randomization with Many Weak Invalid Instruments

Mendelian randomization (MR) has become a popular approach to study causal effects by using genetic variants as instrumental variables. This package implements GENIUS-MAWII. Reference: Ting Ye, Zhonghua Liu, Baoluo Sun, and Eric Tchetgen Tchetgen (2021). GENIUS-MAWII: For Robust Mendelian Randomization with Many Weak Invalid Instruments. Available at https://arxiv.org/abs/2107.06238.

Last updated

1.70 score 1 scripts

ColliderBias - Adjust collider bias and weak instrument bias in Mendelian Randomisation

This package provides adjustment for collider bias and weak instrument bias in association statistics in the context of a genome-wide association study for a subsequent event, using CWLS (Corrected Weighted Least Squares), MR-RAPS and Slope Hunter. An estimation of true causal effect between disease progression and an exposure of interest can be computed using generalised instrument effect regression with CWBLS (Corrected Weighted Bivariate Least Squares).

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1.70 score 1 stars 1 scripts

MRPATH - R Package for MR-PATH

This package implements methods for fitting the MR-PATH model.

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openblascppopenmp

1.70 score 1 scripts

mrcovreg - Package for an efficient and robust approach to Mendelian randomization with measured pleiotropic effects

Implement a method for an efficient and robust approach to Mendelian randomization with measured pleiotropic effects in a high-dimensional setting.

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1.70 score

MRMiSTERI - Mixed-Scale Treatment Effect Robust Identification (MR MiSTERI) and Estimation

This package performs robust Mendelian randomization to estimate the effect of treatment on the treated with possibly invalid IVs.

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1.70 score

sisVIVE - Some Invalid Some Valid Instrumental Variables Estimator

Selects invalid instruments amongst a candidate of potentially bad instruments. The algorithm selects potentially invalid instruments and provides an estimate of the causal effect between exposure and outcome.

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1.68 score 1 stars 12 scripts 180 downloads

hapsim - Haplotype Data Simulation

Package for haplotype-based genotype simulations. Haplotypes are generated such that their allele frequencies and linkage disequilibrium coefficients match those estimated from an input data set.

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1.30 score 1 stars 8 scripts 25 downloads

MRZero - Diet Mendelian Randomization

Encodes several methods for performing Mendelian randomization analyses with summarized data. Similar to the 'MendelianRandomization' package, but with fewer bells and whistles, and less frequent updates. As described in Yavorska (2017) <doi:10.1093/ije/dyx034> and Broadbent (2020) <doi:10.12688/wellcomeopenres.16374.2>.

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1.00 score 151 downloads

iGasso - Statistical Tests and Utilities for Genetic Association

A collection of statistical tests for genetic association studies and summary data based Mendelian randomization.

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1.00 score 6 scripts 221 downloads