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INTERSNP is a software for genome-wide interaction analysis (GWIA) of case-control SNP data and quantitative traits. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information). Our software product implements

 

  • A logistic regression framework as well as log-linear models for joint analysis of multiple SNPs.
  • Automatic handling of SNP annotation and pathway information
  • Methods to account for multiple testing, in particular, Monte-Carlo simulations to judge genome-wide significance.
  • A linear regression framework for analysis of quantitative traits
  • Pathway Association Analysis (SNP ratio, Fisher score, Gene ratio, Fisher Max, Fisher MaxPlus)
  • Genome-wide Haplotype Analysis
  • Pre-tests for quick analysis
  • Pathway Association Analysis with interaction-ratio
  • New features:
    • All PLINK input formats (ped/map, tped/tfam, bed/bim/fam) can be used
    • Considerably improved performance and memory efficiency
    • Case-Only-Analysis

Herold C, Steffens M, Brockschmidt FF, Baur MP, Becker T (2009) INTERSNP: Genome-wide Interaction Analysis Guided by a priori Information. Bioinformatics. 2009 Dec 15;25(24):3275-81