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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12.24 score 560 stars 4 dependents 2.9k 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.
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11.71 score 113 stars 9 dependents 1.1k scripts 2.8k downloadspcaMethods - 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
11.20 score 54 stars 80 dependents 910 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
8.39 score 102 stars 1 dependents 89 scripts 630 downloadsMVMR - MVMR
An R package for performing multivariable Mendelian randomization analyses.
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8.32 score 55 stars 1 dependents 386 scriptsGenomicSEM - Structural equation modeling based on GWAS summary statistics
Later
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7.80 score 300 stars 290 scriptsMendelianRandomization - 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
7.61 score 46 stars 1 dependents 938 scripts 3.1k downloadsOneSampleMR - 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
7.46 score 27 stars 38 scripts 584 downloadsrsnps - 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
7.18 score 55 stars 1 dependents 76 scripts 82 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
6.80 score 21 stars 68 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.
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6.67 score 97 stars 5 dependents 636 scriptsRadialMR - RadialMR
A package for implementing radial inverse variance weighted and MR-Egger methods.
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6.58 score 34 stars 5 dependents 148 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>.
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missing-datamultiple-imputation
6.43 score 8 stars 20 scripts 246 downloadsepigraphdb - 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
6.20 score 31 stars 17 scripts 413 downloadsmrbayes - 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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onetbbcpp
5.85 score 5 stars 9 scripts 449 downloadsgpmapr - Query the OpenGWAS genotype-phenotype map
This package is a simple wrapper around the OpenGWAS genotype-phenotype map API.
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5.76 score 6 stars 16 scriptsCAMeRa - 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
5.68 score 3 stars 396 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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5.48 score 24 stars 1 dependents 12 scriptssimulateGP - Functions for Simulating Genotype-Phenotype Relationships
Functions for simulating SNP effects on phenotypes. Functions for simulating disease risk on probability and liability scales. Simulations to quickly obtain estimates of effect sizes for simulated genotype-phenotypes.
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geneticssimulationsstatistics
5.41 score 9 stars 238 scriptsMRInstruments - Data sources for genetic instruments to be used in MR
Datasets of eQTLs, GWAS catalogs, etc.
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5.34 score 49 stars 299 scriptsMRMix - 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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5.23 score 25 stars 5 dependents 91 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.
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5.19 score 13 stars 1 dependents 79 scriptsalspac - Data dictionary for ALSPAC
Functions to search and extract variables based on keywords from the ALSPAC data dictionary.
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5.17 score 12 stars 44 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:10.1080/01621459.1997.10474074>). 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
5.09 score 19 scripts 485 downloadstriangulate - Useful functions for performing evidence triangulation
What the package does (one paragraph).
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5.03 score 4 stars 10 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.
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4.97 score 11 stars 168 scripts 583 downloadsGWASBrewer - Simulate Realistic GWAS Summary Statistics
Simulate GWAS summary statistics from specified DAG or factor structure.
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openblascpp
4.95 score 12 stars 25 scriptsgenepi.utils - GenEpi Utility Functions
The genepi.utils package is a collection of utility functions for working with genetic epidemiology data.
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4.93 score 11 stars 11 scriptsEpiViz - 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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4.90 score 9 stars 44 scripts
nlmr - Non-linear Mendelian randomisation
Non-linear Mendelian randomization analysis to investigate the shape of exposure-outcome relationships.
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4.84 score 56 stars 247 scriptscause - CAUSE: Causal Analysis Using Summary Effect Estimates
Identify causal patterns using pairs of GWAS summary statistics.
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cpp
4.76 score 59 stars 196 scriptshdi - High-Dimensional Inference
Implementation of multiple approaches to perform inference in high-dimensional models.
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4.57 score 2 stars 5 dependents 249 scripts 264 downloadsRMVMR - RMVMR
An R package for performing radial multivariable Mendelian randomization analyses.
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4.29 score 13 stars 15 scripts
geni.plots - GENI plots
GENI plots is designed to visualise results from genome-wide association studies.
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4.20 score 32 starssimmrd - 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 scriptsSUMnlmr - 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 scriptsaciccomp2016 - Atlantic Causal Inference Conference Competition 2016 Simulation
Generate simulation data.
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3.76 score 46 stars 25 scriptsMRcML - Mendelian randomization method with constrained maximum likelihood.
Perform MRcML method.
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3.59 score 15 stars 52 scriptsmrclust - 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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3.52 score 19 stars 35 scriptsBWMR - Bayesian Weighted Mendelian Randomization (BWMR)
Inference the causality based on BWMR method.
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3.29 score 39 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.
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openblascppopenmp
3.28 score 2 stars 19 scripts 221 downloadsFLOWMR - 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 scriptsproxysnps - 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 10 scriptsmrbma - 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 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.
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3.02 score 21 stars 1 scriptstryx - 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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3.00 score 10 stars 9 scriptsvarGWASR - 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 starsscreening - What the Package Does (one line, title case)
What the package does (one paragraph).
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2.81 score 13 stars 3 scriptsmrlocus - 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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onetbbcpp
2.78 score 1 stars 12 scriptsMVMRcML - 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 scriptstmsens - 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 5 scripts 335 downloadsFusioMR - 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
2.60 score 2 stars 4 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
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 scriptsjournalclub - Journal club papers
Uses citations and PubMed queries to generate new publications for a journal club.
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1.78 score 12 scriptsRMR.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
1.70 score 2 scriptsMVMR.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
1.70 score 1 scripts
gassocplot - Regional association plots
This package is used plot regional association plots.
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1.70 scoreMRPATH - R Package for MR-PATH
This package implements methods for fitting the MR-PATH model.
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openblascppopenmp
1.70 score 1 scriptssisVIVE - 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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1.64 score 1 stars 11 scripts 225 downloadsiGasso - 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 262 downloads