SNPsea

SNPsea is a C++ implementation of a single-nucleotide polymorphism (SNP) set enrichment algorithm that identifies cell types, tissues, and pathways affected by risk loci. It uses a non-parametric statistical approach to compute empirical p-values by comparison with null SNP sets. SNPsea is available at http://broadinstitute.org/mpg/snpsea, and it has been applied to four sets of genome-wide significant SNPs associated with red blood cell count, multiple sclerosis, celiac disease, and HDL cholesterol. Supplementary data are available at Bioinformatics online.

Topic

Functional genomics

Detail

  • Operation: Gene-set enrichment analysis

  • Software interface: Command-line user interface

  • Language: R;C++;Python

  • License: Other

  • Cost: Free

  • Version name: v1.0.3

  • Credit: The National Institutes of Health, the Arthritis Foundation, the Doris Duke Foundation.

  • Input: -

  • Output: -

  • Contact: Kamil Slowikowski slowikow@broadinstitute.org, Soumya Raychaudhuri soumya@broadinstitute.org

  • Collection: -

  • Maturity: Stable

Publications

  • SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci.
  • Slowikowski K, et al. SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci. SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci. 2014; 30:2496-7. doi: 10.1093/bioinformatics/btu326
  • https://doi.org/10.1093/bioinformatics/btu326
  • PMID: 24813542
  • PMC: PMC4147889

Download and documentation

< Back to DB search