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 2 months ago

11.17 score 429 stars 1 packages 1.7k scripts

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 3 months ago

10.61 score 76 stars 5 packages 350 scripts 3.8k downloads

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

5.85 score 68 stars 2 packages 116 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 1 years ago

5.33 score 9 stars 3 packages 53 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 8 months ago

causal-inferencegwas-summary-statisticsmendelian-randomisationmulti-ancestry

5.29 score 2 stars 163 scripts

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

Datasets of eQTLs, GWAS catalogs, etc.

Last updated 4 years ago

5.13 score 43 stars 210 scripts

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

4.66 score 117 stars 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 2 years ago

4.37 score 3 stars 13 scripts