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 10 days ago

421 stars 11.16 score 112 dependencies 1 dependents

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.

Last updated 2 months ago

72 stars 10.55 score 23 dependencies 5 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 1 years ago

66 stars 5.73 score 84 dependencies 2 dependents

CAMeRa - CAMeRa (Cross Ancestral Mendelian Randomisation)

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

Last updated 6 months ago

causal-inferencegwas-summary-statisticsmendelian-randomisationmulti-ancestry

2 stars 5.31 score 44 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 1 years ago

9 stars 5.18 score 0 dependencies 3 dependents

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

Datasets of eQTLs, GWAS catalogs, etc.

Last updated 4 years ago

43 stars 5.13 score 0 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 3 years ago

112 stars 4.63 score 188 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 4.37 score 171 dependencies