## TwoSampleMR - Two Sample MR Functions and Interface to MR Base Database

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

Last updated 1 months ago

404 stars 6.96 score 112 dependencies 1 dependents## GenomicSEM - Structural equation modeling based on GWAS summary statistics

Later

Last updated 30 days ago

192 stars 5.45 score 54 dependencies## 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.

Last updated 3 years ago

4 stars 4.80 score 54 dependencies## 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.

Last updated 2 years ago

108 stars 4.15 score 188 dependencies## ieugwasr - Interface to the 'OpenGWAS' Database API

Interface to the 'OpenGWAS' database API <https://gwas-api.mrcieu.ac.uk/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.

Last updated 1 months ago

69 stars 4.13 score 23 dependencies 5 dependents## 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.

Last updated 1 years ago

79 stars 3.78 score 0 dependencies 2 dependents## 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.

Last updated 11 months ago

64 stars 3.52 score 84 dependencies 2 dependents## cause - CAUSE: Causal Analysis Using Summary Effect Estimates

Identify causal patterns using pairs of GWAS summary statistics.

Last updated 3 years ago

52 stars 3.00 score 67 dependencies## nlmr - Non-linear Mendelian randomisation

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

Last updated 7 months ago

49 stars 2.94 score 34 dependencies## 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.

Last updated 4 months ago

42 stars 2.83 score 88 dependencies 1 dependents## MRInstruments - Data sources for genetic instruments to be used in MR

Datasets of eQTLs, GWAS catalogs, etc.

Last updated 4 years ago

42 stars 2.76 score 0 dependencies## MVMR - MVMR

An R package for performing multivariable Mendelian randomization analyses.

Last updated 1 years ago

40 stars 2.63 score 1 dependencies## GRAPPLE - R Package for MR Framework GRAPPLE

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

Last updated 5 months ago

35 stars 2.53 score 75 dependencies## RadialMR - RadialMR

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

Last updated 1 years ago

29 stars 2.46 score 70 dependencies 2 dependents## 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 HernĂ¡n 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>.

Last updated 1 months ago

instrumental-variableinstrumental-variablesmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomization

15 stars 2.45 score 68 dependencies## causl - Methods for Specifying, Simulating from and Fitting Causal Models

Model multivariate distributions using causal parameters.

Last updated 3 days ago

12 stars 2.31 score 23 dependencies## 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.

Last updated 2 years ago

api-clientbioinformaticsepidemiologygraph-databasemendelian-randomizationphenotypes

25 stars 2.28 score 20 dependencies## geni.plots - GENI plots

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

Last updated 1 months ago

20 stars 2.27 score 66 dependencies## 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.

Last updated 9 months ago

15 stars 2.22 score 16 dependencies 3 dependents## 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.

Last updated 5 years ago

22 stars 2.14 score 0 dependencies 2 dependents## genepi.utils - GenEpi Utility Functions

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

Last updated 15 days ago

5 stars 2.09 score 188 dependencies## SUMnlmr - Non-Linear Mendelian Randomization On Partially Summarized Data

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

Last updated 2 months ago

19 stars 1.90 score 39 dependencies## 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:10.2307/2965583>). 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).

Last updated 2 months ago

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

1.84 score 0 dependencies## alspac - Data dictionary for ALSPAC

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

Last updated 7 days ago

11 stars 1.80 score 34 dependencies## mrbma - Mendelian Randomization Bayesian Model Averaging

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

Last updated 1 years ago

21 stars 1.80 score 119 dependencies## 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>.

Last updated 2 years ago

6 stars 1.76 score 171 dependencies## 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.

Last updated 5 months ago

19 stars 1.75 score 133 dependencies## 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.

Last updated 11 months ago

9 stars 1.75 score 0 dependencies 3 dependents## 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 whether multiple imputation is needed, and if so, how best to perform it.

Last updated 2 hours ago

missing-datamultiple-imputation

6 stars 1.69 score 114 dependencies## 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.

Last updated 3 months ago

4 stars 1.64 score 7 dependencies## GWASBrewer - Simulate Realistic GWAS Summary Statistics

Simulate GWAS summary statistics from specified DAG or factor structure.

Last updated 4 months ago

5 stars 1.64 score 27 dependencies## 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.

Last updated 5 months ago

3 stars 1.64 score 70 dependencies## 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.

Last updated 1 years ago

9 stars 1.48 score 34 dependencies## 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.

Last updated 3 months ago

1 stars 1.31 score 107 dependencies## DRMR - Doubly-Ranked Stratification in Mendelian Randomization

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

Last updated 3 months ago

6 stars 1.31 score 116 dependencies## 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.

Last updated 4 months ago

5 stars 1.31 score 13 dependencies## RMVMR - RMVMR

An R package for performing radial multivariable Mendelian randomization analyses.

Last updated 1 years ago

12 stars 1.31 score 73 dependencies## 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.

Last updated 1 years ago

8 stars 1.24 score 138 dependencies 1 dependents## 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.

Last updated 3 years ago

11 stars 1.24 score 89 dependencies## MRcML - Mendelian randomization method with constrained maximum likelihood.

Perform MRcML method.

Last updated 3 years ago

12 stars 1.24 score 0 dependencies## MVMRcML - Multivariable Mendelian randomization based on constrained maximum likelihood

Robust multivariable Mendelian randomization based on constrained maximum likelihood.

Last updated 4 months ago

9 stars 1.16 score 3 dependencies## 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.

Last updated 5 months ago

4 stars 1.16 score 28 dependencies## 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.

Last updated 2 years ago

11 stars 1.16 score 48 dependencies## 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.

Last updated 4 years ago

10 stars 1.16 score 114 dependencies## 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.

Last updated 5 years ago

2 stars 1.10 score 2 dependencies## EpiViz - An implementation of Circos plots for epidemiologists

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.

Last updated 9 months ago

9 stars 1.08 score 37 dependencies## mrSampleOverlap - Estimate Bias Due To Sample Overlap In Mendelian Randomization Studies

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

Last updated 2 years ago

10 stars 1.08 score 16 dependencies## mrsensemakr - Sensitivity Analysis Tools for Mendelian Randomization

The R package mrsensemakr implements sensitivity analysis tools for Mendelian Randomization.

Last updated 3 years ago

9 stars 1.00 score 1 dependencies## 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.

Last updated 3 months ago

0.91 score 132 dependencies## CAMeRa - CAMeRa (Cross Ancestral Mendelian Randomisation)

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

Last updated 4 months ago

causal-inferencegwas-summary-statisticsmendelian-randomisationmulti-ancestry

2 stars 0.82 score 44 dependencies## MR.CUE - What the package does (short line)

More about what it does (maybe more than one line)

Last updated 9 months ago

4 stars 0.82 score 4 dependencies## tmsens - Sensitivity Analysis Using the Trimmed Means Estimator

Sensitivity analysis using the trimmed means estimator.

Last updated 1 years ago

missing-datasensitivity-analysistrimmed-means

0.73 score 0 dependencies## MrDAG - MrDAG: Mendelian randomization (MR) with Bayesian Directed Acyclic (DAG) Graphs exploration and causal effects estimation

This package performs Mendelian randomization for multiple exposures and outcomes with Bayesian Directed Acyclic Graphs exploration and causal effects estimation.

Last updated 2 months ago

4 stars 0.71 score 18 dependencies## lmrse - Linear regression with clustered robust standard errors

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

Last updated 7 months ago

3 stars 0.61 score 5 dependencies## 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.

Last updated 1 years ago

3 stars 0.61 score 171 dependencies## BESIDEMR - BayEsian Set IDEntification Mendelian randomization

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

Last updated 2 years ago

5 stars 0.61 score 0 dependencies## MR.Corr2 - 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.

Last updated 3 years ago

4 stars 0.61 score 6 dependencies## 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.

Last updated 9 months ago

1 stars 0.49 score 6 dependencies## metaboprep - Metabolomics data preparation and processing pipeline

Reads in raw Metabolon and Nightingale xls sheets and aids in data preparation of all metabolomics data sets.

Last updated 5 months ago

0.36 score 87 dependencies## MrMediation - An R Package for Mendelian Randomization in the mediation setting

A Bayesian framework for Mendelian Randomization in the mediation setting.

Last updated 5 months ago

0.36 score 37 dependencies## jlst - Joint location-and-scale tests

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

Last updated 7 months ago

2 stars 0.36 score 7 dependencies## 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.

Last updated 12 months ago

1 stars 0.23 score 53 dependencies## 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.

Last updated 4 years ago

2 stars 0.36 score 0 dependencies## 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>.

Last updated 4 months ago

0.23 score 82 dependencies## MRPATH - R Package for MR-PATH

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

Last updated 5 months ago

0.23 score 77 dependencies## finemapr - R wrapper to fine-mappers

R wrapper to fine-mappers.

Last updated 7 months ago

0.23 score 46 dependencies## 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

Last updated 2 years ago

2 stars 0.23 score 42 dependencies## 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 .

Last updated 3 years ago

2 stars 0.23 score 66 dependencies## BWMR - Bayesian Weighted Mendelian Randomization (BWMR)

Inference the causality based on BWMR method.

Last updated 2 months ago

0.09 score 28 dependencies## iGasso - Statistical Tests and Utilities for Genetic Association

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

Last updated 5 months ago

0.09 score 34 dependencies## 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.

Last updated 5 months ago

0.09 score 10 dependencies## 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.

Last updated 4 years ago

1 stars 0.09 score 91 dependencies## 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.

Last updated 7 years ago

1 stars 0.09 score 1 dependencies## journalclub - Journal club papers

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

Last updated 1 years ago

0.00 score 3 dependencies## varGWASR - Least Absolute Deviation Regression Brown Forsythe Test

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

Last updated 2 years ago

geneticsheteroscedasticityheteroskedasticitystatisticsvariance

1 stars 0.00 score 64 dependencies