SNPsea Manual

Github project: https://github.com/slowkow/snpsea

• Introduction
• Visual Summary
  • Cartoon
  • Flow Chart
• Algorithm Details
  • Step 1: Assigning genes to each SNP
  • Step 2: Calculating specificity scores
  • Step 3: Testing significance
  • Example
• Installation
  • C++ Libraries
  • Python Packages
  • R Packages
• Data
  • SNP sets
  • Gene matrices
  • LD-pruned SNPs and Genomic Intervals
• Usage
  • Options
  • Input File Formats
  • Output Files
• Output Visualizations
  • View enrichment of tissue-specific gene expression
  • View the most specifically expressed gene for each SNP-tissue pair
  • View the type 1 error rate estimates for each tissue
• Supplementary Figures
  • Supplementary Figure 1: Determining SNP linkage intervals
  • Supplementary Figure 2: Counting genes in GWAS SNP linkage intervals
  • Supplementary Figure 3: Choosing the \(r^{2}\) threshold for linkage intervals
  • Supplementary Figure 4: Each trait-associated locus harbors a single associated gene
  • Supplementary Figure 5: Type 1 error estimates
  • Supplementary Figure 6: Red blood cell count GO enrichment
  • Supplementary Figure 7: Multiple sclerosis
  • Supplementary Figure 8: Celiac disease
  • Supplementary Figure 9: HDL cholesterol
• References