SNPSEA: a SNP Set Enrichment algorithm to identify cell types, tissues and pathways affected by risk loci

·112 words·1 min
C++
Table of Contents

SNPSEA
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SNPSEA is a single-nucleotide polymorphism (SNP) Set Enrichment Algorithm (SEA) to identify which cell types preferentially express the genes that are associated with a trait.

Input files:

  • A list of genome-wide significant SNP identifiers (e.g. rs42) from a genome-wide association study (GWAS) on your preferred trait.
  • A (NxM) matrix of gene expression values for all genes (N) across a large number (M) of cell types.
slowkow/snpsea

📊 Identify cell types and pathways affected by genetic risk loci.

C++
36
9

Example
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Figure 1

SNPSEA compares the trait-associated single-nucleotide polymorphisms (SNPs) to randomly sampled SNPs while accounting for linkage disequilibrium (LD). It’s implemented in C++ with executables available for macOS or Linux.

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