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 3 months ago
11.16 score 440 stars 1 dependents 1.7k scriptsieugwasr - 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.
Last updated 4 months ago
10.61 score 76 stars 5 dependents 350 scripts 3.8k downloadsMendelianRandomization - 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 8 months ago
7.55 score 44 stars 1 dependents 896 scripts 3.0k downloadsGenomicSEM - Structural equation modeling based on GWAS summary statistics
Later
Last updated 1 days ago
7.09 score 210 stars 112 scriptscausl - Methods for Specifying, Simulating from and Fitting Causal Models
Model multivariate distributions using causal parameters.
Last updated 15 days ago
fortranopenblascppopenmp
6.68 score 12 stars 33 scriptsOneSampleMR - 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 4 months ago
instrumental-variableinstrumental-variablesmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomization
6.64 score 18 stars 16 scripts 236 downloadsMVMR - MVMR
An R package for performing multivariable Mendelian randomization analyses.
Last updated 2 months ago
6.49 score 44 stars 1 dependents 155 scriptsRadialMR - RadialMR
A package for implementing radial inverse variance weighted and MR-Egger methods.
Last updated 2 months ago
5.91 score 33 stars 3 dependents 110 scriptsepigraphdb - 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
5.91 score 27 stars 9 scripts 289 downloadsgenepi.utils - GenEpi Utility Functions
The genepi.utils package is a collection of utility functions for working with genetic epidemiology data.
Last updated 2 months ago
5.88 score 9 stars 8 scriptsgwasvcf - 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 1 years ago
5.85 score 68 stars 2 dependents 116 scriptsgwasglue2 - 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 1 years ago
5.82 score 19 stars 3 dependents 11 scriptsMRPRESSO - 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
5.76 score 83 stars 2 dependents 232 scriptsmidoc - 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>.
Last updated 2 months ago
missing-datamultiple-imputation
5.56 score 6 stars 8 scripts 156 downloadsGWASBrewer - Simulate Realistic GWAS Summary Statistics
Simulate GWAS summary statistics from specified DAG or factor structure.
Last updated 1 months ago
5.41 score 8 stars 27 scriptsCAMeRa - CAMeRa (Cross Ancestral Mendelian Randomisation)
CAMERA estimates joint causal effect in multiple ancestries and detects pleiotropy via the zero relevance model.
Last updated 8 months ago
causal-inferencegwas-summary-statisticsmendelian-randomisationmulti-ancestry
5.30 score 2 stars 165 scriptsgenetics.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 1 years ago
5.16 score 9 stars 2 dependents 53 scriptsMRInstruments - Data sources for genetic instruments to be used in MR
Datasets of eQTLs, GWAS catalogs, etc.
Last updated 4 years ago
5.14 score 43 stars 212 scriptsGwasDataImport - 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 4 days ago
5.09 score 3 stars 13 scriptsmrbayes - 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 4 months ago
cpp
5.08 score 4 stars 2 scripts 316 downloadsnlmr - Non-linear Mendelian randomisation
Non-linear Mendelian randomization analysis to investigate the shape of exposure-outcome relationships.
Last updated 11 months ago
5.02 score 54 stars 194 scriptsgeni.plots - GENI plots
GENI plots is designed to visualise results from genome-wide association studies.
Last updated 2 months ago
5.01 score 23 stars 7 scriptsalspac - Data dictionary for ALSPAC
Functions to search and extract variables based on keywords from the ALSPAC data dictionary.
Last updated 21 days ago
4.93 score 11 stars 47 scriptsbpbounds - 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 4 months ago
aceaverage-causal-effectboundsinstrumental-variableivmendelianmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomizationmrnonparametricnonparametric-boundspearlshiny
4.92 score 12 scripts 645 downloadsMRPC - 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 3 years ago
4.70 score 8 stars 21 scripts 297 downloadsMRMix - 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
4.68 score 24 stars 2 dependents 66 scriptsgwasglue - 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 3 years ago
4.66 score 117 stars 79 scriptsivmodel - 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 2 years ago
4.62 score 9 stars 93 scripts 495 downloadshdi - High-Dimensional Inference
Implementation of multiple approaches to perform inference in high-dimensional models.
Last updated 4 years ago
4.50 score 2 stars 7 dependents 134 scripts 1.1k downloadscause - CAUSE: Causal Analysis Using Summary Effect Estimates
Identify causal patterns using pairs of GWAS summary statistics.
Last updated 3 years ago
4.39 score 53 stars 93 scriptssimmrd - 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 9 months ago
4.13 score 3 starsmrSampleOverlap - 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
3.74 score 11 starsmrsensemakr - Sensitivity Analysis Tools for Mendelian Randomization
The R package mrsensemakr implements sensitivity analysis tools for Mendelian Randomization.
Last updated 3 years ago
3.65 score 9 stars 6 scriptsMrMediation - An R Package for Mendelian Randomization in the mediation setting
A Bayesian framework for Mendelian Randomization in the mediation setting.
Last updated 25 days ago
3.45 score 7 starsGRAPPLE - R Package for MR Framework GRAPPLE
Fitting and diagnosing two-sample summary data Mendelian randomization with heterogeneous instruments.
Last updated 9 months ago
3.43 score 36 stars 15 scriptsSUMnlmr - Non-Linear Mendelian Randomization On Partially Summarized Data
Runs non-linear MR calculations on partly-summarized data.
Last updated 7 months ago
3.42 score 22 stars 12 scriptsCheckSumStats - 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 2 years ago
3.42 score 7 stars 1 dependents 25 scriptsprop.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 9 months ago
3.38 score 4 stars 1 scriptsDRMR - 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 4 months ago
3.38 score 8 stars 4 scriptsRMVMR - RMVMR
An R package for performing radial multivariable Mendelian randomization analyses.
Last updated 2 months ago
3.37 score 12 stars 13 scriptsMRcML - Mendelian randomization method with constrained maximum likelihood.
Perform MRcML method.
Last updated 4 months ago
3.36 score 13 stars 35 scriptsBWMR - Bayesian Weighted Mendelian Randomization (BWMR)
Inference the causality based on BWMR method.
Last updated 6 months ago
3.30 score 40 scriptsPPMR - 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
3.28 score 2 stars 19 scripts 115 downloadslhcMR - 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 9 months ago
3.10 score 23 stars 11 scriptsmrbma - Mendelian Randomization Bayesian Model Averaging
A set of functions designed to implement Mendelian Randomization Bayesian Model Averaging.
Last updated 2 years ago
3.02 score 21 stars 2 scriptsEpiViz - 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 1 years ago
2.91 score 9 stars 18 scriptsTVMR - 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 2 months ago
2.90 score 2 stars 1 scriptsMR2 - 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
2.90 score 16 starsMrDAG - 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 1 months ago
2.88 score 5 starsmrclust - 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
2.85 score 13 stars 11 scriptsscreening - What the Package Does (one line, title case)
What the package does (one paragraph).
Last updated 9 years ago
2.81 score 13 stars 7 scriptstmsens - Sensitivity Analysis Using the Trimmed Means Estimator
Sensitivity analysis using the trimmed means estimator.
Last updated 4 months ago
missing-datasensitivity-analysistrimmed-means
2.70 score 1 stars 1 scripts 177 downloadsmr.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>.
Last updated 8 months ago
2.70 score 1 scripts 206 downloadsmrlocus - 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 1 years ago
cpp
2.70 score 1 stars 9 scriptsvarGWASR - Least Absolute Deviation Regression Brown Forsythe Test
Brown-Forsythe SNP test using LAD regression and variance effect estimate
Last updated 2 years ago
geneticsheteroscedasticityheteroskedasticitystatisticsvariance
2.70 score 1 starstryx - 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
2.70 score 10 stars 9 scriptsMVMRcML - Multivariable Mendelian randomization based on constrained maximum likelihood
Robust multivariable Mendelian randomization based on constrained maximum likelihood.
Last updated 8 months ago
openblascpp
2.65 score 9 stars 4 scriptslmrse - 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 11 months ago
cpp
2.48 score 3 stars 1 scriptsBESIDEMR - BayEsian Set IDEntification Mendelian randomization
The R package to perform BayEsian Set IDEntification Mendelian randomization (BESIDE-MR).
Last updated 2 years ago
2.40 score 5 starsMR.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
openblascppopenmp
2.34 score 4 stars 11 scriptsMR.CUE - What the package does (short line)
More about what it does (maybe more than one line)
Last updated 1 years ago
openblascppopenmp
2.30 score 4 stars 10 scriptsindexevent - 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 3 months ago
2.28 score 2 stars 19 scriptsRFQT - 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 7 months ago
2.18 score 1 scriptsmetaboprep - 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 9 months ago
2.00 score 7 scriptsjlst - Joint location-and-scale tests
Joint location-and-scale tests for joint testing of mean (location) and variance (scale).
Last updated 11 months ago
2.00 score 2 starsMR.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 1 years ago
openblascppopenmp
1.88 score 1 stars 15 scriptsMRPATH - R Package for MR-PATH
This package implements methods for fitting the MR-PATH model.
Last updated 9 months ago
openblascppopenmp
1.70 score 1 scriptsfinemapr - R wrapper to fine-mappers
R wrapper to fine-mappers.
Last updated 11 months ago
1.70 score 6 scriptsjournalclub - Journal club papers
Uses citations and PubMed queries to generate new publications for a journal club.
Last updated 2 years ago
1.70 score 9 scriptsMRTool - 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 5 years ago
1.70 score 1 starssisVIVE - 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 8 years ago
1.64 score 1 stars 11 scripts 175 downloadsMRZero - 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 8 months ago
1.00 score 167 downloadsiGasso - Statistical Tests and Utilities for Genetic Association
A collection of statistical tests for genetic association studies and summary data based Mendelian randomization.
Last updated 9 months ago
1.00 score 6 scripts 233 downloads