Welcome to Mendelian Randomization Analysis

MRanalysis is an interactive R Shiny application designed for Mendelian randomization analysis.

Introduction

Mendelian randomization (MR) has emerged as a powerful epidemiological method for inferring causal relationships between exposures and outcomes using genome-wide association study (GWAS) summary data. By leveraging instrumental variables (IVs), such as single nucleotide polymorphisms (SNPs), MR can revolutionize our understanding of disease etiology, inform public health strategies, and accelerate drug discovery.

However, the widespread adoption of MR is hindered by several challenges, including inconsistent GWAS data formats, lack of standardized workflows, the need for extensive programming expertise, and limitations in data visualization and interpretability. To address these challenges, we introduce MRanalysis , a comprehensive and user-friendly, web-based platform that provides the first integrated and standardized MR analysis workflow. This includes GWAS data quality assessment, power/ sample size estimation, MR analysis, SNP-to-gene enrichment analysis, and data visualization. Built using the R shiny framework, MRanalysis enables users to conduct common MR methods, including univariable, multivariable, and mediation MR analyses through an intuitive, no-code interface .

Besides MRanalysis, we developed GWASkit , a standalone, and installation-free tool facilitating rapid GWAS dataset preprocessing before MR analyses, including rs ID conversion, format standardization, and data extraction, with significantly lower conversion time and dramatically higher rs ID conversion accuracy than the current tools. Case studies demonstrate the utility, efficiency, and ease of use of our developed platform and GWASkit tool in real-world scenarios. By lowering barriers to investigating causal genetic relationships, our platform represents a significant advance in making MR more accessible, reliable, and efficient. The increased adoption of MR, facilitated by MRanalysis and GWASkit, can accelerate discoveries in genetic epidemiology, strengthen evidence-based public health strategies, and guide the development of targeted clinical interventions.

Quick Links

Doing MR analysis and visualization without coding expertise.

  • All
  • MR (API)
  • MR (Local)
  • Plugins
  • Plugins (GWASkit)
  • Data Visualization

Two sample Mendelian randomization

Two sample Mendelian randomization (2SMR) is a method to estimate the causal effect of an exposure on an outcome using only summary statistics from genome wide association studies (GWAS).

Multivariable Mendelian Randomization

Multivariable Mendelian Randomisation (MVMR) is a form of instrumental variable analysis which estimates the direct effect of multiple exposures on an outcome using genetic variants as instruments.

Mediation Mendelian Randomization

Mediation analysis seeks to explain the pathway(s) through which an exposure affects an outcome.

Two sample Mendelian randomization

Two sample Mendelian randomization (2SMR) is a method to estimate the causal effect of an exposure on an outcome using only summary statistics from genome wide association studies (GWAS).

Multivariable Mendelian Randomization

Multivariable Mendelian Randomisation (MVMR) is a form of instrumental variable analysis which estimates the direct effect of multiple exposures on an outcome using genetic variants as instruments.

Mediation Mendelian Randomization

Mediation analysis seeks to explain the pathway(s) through which an exposure affects an outcome.

CheckSumStats

This application for the identification of errors and analytical issues in the results and metadata of genome-wide association studies (GWAS).

Power Calculator

This plugin is used to calculate statistical power in Mendelian randomization studies.

Sample Size Calculator

This statistical calculator determines the minimum sample size required for adequate statistical power in a study by applying various equations.

SNP gene mapping and enrichment

This plugin uses MAGMA for SNP gene mapping and enrichment analysis and gene set evaluations.

GO enrichment analysis

Gene Ontology (GO) term enrichment is a technique for interpreting sets of genes making use of the Gene Ontology system of classification, in which genes are assigned to a set of predefined bins depending on their functional characteristics.

KEGG enrichment analysis

KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis is a popular bioinformatics method used to identify biological pathways that are significantly enriched in a set of genes or proteins.

Universal Enrichment Analysis

A universal enrichment analyzer

GWAS Data Format Standardization

The plugin provides a tool for standard format conversion of GWAS summary data, ensuring that data from different GWAS databases can be used for MR analysis on this platform.

rs ID Conversion

This plugin can match corresponding SNP IDs based on CHR, POS, REF, and ALT.

VCF to TSV

This plugin can convert VCF format to TSV format and extract specified information.

Forest Plot

Forest plots illustrate study relationships, consistency, precision, and heterogeneity in meta-analysis results.

Forest Plot (MVMR)

Forest plots illustrate study relationships, consistency, precision, and heterogeneity in meta-analysis results.

Manhattan Plot

A Manhattan plot in GWAS displays numerous significant SNPs with varying magnitudes for identifying genetic associations.

Q-Q Plot

In statistics, a Q–Q plot (quantile–quantile plot) is a probability plot, a graphical method for comparing two probability distributions by plotting their quantiles against each other.

Pie Chart

A piechart is a circle divided into sectors that each represent a proportion of the whole.

Venn Diagram

A Venn diagram is an illustration that uses overlapping circles to show the logical relationship between two or more sets of items.

Circos Plot (GO)

The Circos plot representation of GO-Annotation terms of genes in a) Biological Process b) Cellular Components c) Molecular Function.

Dot Plot (GO)

The Dot plot representation of GO-Annotation terms of genes in a) Biological Process b) Cellular Components c) Molecular Function.

Bar Plot (GO)

The Bar plot representation of GO-Annotation terms of genes in a) Biological Process b) Cellular Components c) Molecular Function.

Bar Plot (GO)

The Bar plot representation of GO-Annotation terms of genes in a) Biological Process b) Cellular Components c) Molecular Function.

CircosG Plot CircosG plot in mediation analysis refers to a Directed Acyclic Graph (DAG), which is used to visually represent causal relationships between variables.

Circos Plot (KEGG)

A Circos plot is a circular visualization tool often used to display complex relationships in genomic data, including KEGG pathway interactions.

Bar Plot (KEGG)

A bar plot in the context of KEGG (Kyoto Encyclopedia of Genes and Genomes) is a graphical representation used to display quantitative data related to pathways, such as gene expression levels or pathway enrichment scores.

Bar Plot (KEGG)

A bar plot in the context of KEGG (Kyoto Encyclopedia of Genes and Genomes) is a graphical representation used to display quantitative data related to pathways, such as gene expression levels or pathway enrichment scores.

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