What has changed | Dataset IDs | Authentication | UKBiobank data has been curated | All data is now harmonised | LD reference panel is now harmonised | Instrument lists are up-to-date | dbSNP rs IDs | Everything is faster | What is new | Browse available datasets online | Chromosome and position | INDELs are retained | Multi-allelic variants are retained | More data | Error messages are more informative | Easier programmatic access to the database | Local LD operations | Access the data directly | Connect the data to different analytical tools | Key links | How to request new data

Introduction | MR methods | Sensitivity analyses | Heterogeneity statistics | Horizontal pleiotropy | Single SNP analysis | Leave-one-out analysis | Plots | Scatter plot | Forest plot | Forest plot with categories | RadialMR outlier example | MR-PRESSO outlier example | Leave-one-out plot | Funnel plot | 1-to-many forest plot | Step 1: Generate 1-to-many MR results | Step 2: Make the 1-to-many forest plot | Example 1. Effect of multiple risk factors on coronary heart disease | Example 2. MR results for multiple MR methods grouped by multiple exposures | Example 3. Stratify results on a grouping variable | Example 4. Effect of BMI on 103 diseases | MR-RAPS: Many weak instruments analysis | MR-GRIP | Reports | MR Steiger directionality test | Multivariable MR | Note about multivariable methods | Note about visualisation | Using your own summary data | From local files | From data frames | Mixing local and OpenGWAS data | Converting to MVMR format | MR estimates when instruments are correlated | MR-MoE: Using a mixture of experts machine learning approach | Post MR results management | Split outcome names | Split exposure names | Generate odds ratios with 95% confidence intervals | Subset on method | Combine all results | References

Introduction | Reading in from a file | Example 1: The default column names are used | Example 2: The text file has non-default column names | Using an existing data frame | Obtaining instruments from existing catalogues | GWAS catalog | Metabolites | Proteins | Gene expression levels | DNA methylation levels | IEU OpenGWAS database | Clumping

Introduction | Dealing with strand issues | Correct, unambiguous | Incorrect reference, unambiguous | Ambiguous | Palindromic SNP, inferrable | Palindromic SNP, not inferrable | Options | Drop duplicate exposure-outcome summary sets

Background | Installation | Overview | Authentication | References

Available studies in IEU GWAS database | Extracting particular SNPs from particular studies | LD proxies | Using local GWAS summary data | Outcome data format | More advanced use of local data

Overview | Method | Data & Gene Setup | Run SKO | Interpret Outputs | Caveats | Real-World Example: LRRK2 in VKH Disease | Load pre-computed FIP result | Understanding the comparison direction | Cell-type composition of ghigh | Differential expression summary | GSEA enrichment (GO)

Overview | Prerequisites | Troubleshooting Dependencies | 1. Bioconductor Dependencies | 2. GitHub-Hosted Dependencies | Verification

Aim | Recommended path (2026-02) | Fallback commands for common failures | Verify installation | Notes