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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.

Last updated

12.24 score 560 stars 4 dependents 2.9k 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.

Last updated

7.24 score 111 stars 172 scripts

gpmapr - Query the OpenGWAS genotype-phenotype map

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

Last updated

5.76 score 6 stars 16 scripts

CAMeRa - CAMeRa (Cross Ancestral Mendelian Randomisation)

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

Last updated

causal-inferencegwas-summary-statisticsmendelian-randomisationmulti-ancestry

5.68 score 3 stars 396 scripts

simulateGP - 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.

Last updated

geneticssimulationsstatistics

5.41 score 9 stars 238 scripts

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

Datasets of eQTLs, GWAS catalogs, etc.

Last updated

5.34 score 49 stars 299 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.

Last updated

5.19 score 13 stars 1 dependents 79 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.

Last updated

5.08 score 3 stars 19 scripts

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

3.00 score 10 stars 9 scripts