The SNPchip R package implements classes and methods useful for storing, visualizing, and analyzing high density SNP data. SNPchip was inspired by the SNPscan webtool, and has been written by Drs. Robert Scharpf and Ingo Ruczinski in the Dept. of Biostatistics, Johns Hopkins Bloomberg School of Public Health (in collaboration with Jason Ting and Jonathan Pevsner). The R package SNPchip is freely available from the Bioconductor webpage, and the paper describing SNPchip is in PubMed here.

Links: main SNP databases and resources

  • dbSNP A database of SNPs and other variations at NCBI
  • The SNP Consortium "The SNP Consortium (TSC) is a public/private collaboration that has to date discovered and characterized nearly 1.8 million SNPs."
  • International HapMap project "The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals."

Links: information on SNPs

Links: other software to visualize SNPs

  • Affymetrix SNPscan is designed to use data from SNP mapping arrays from Affymetrix (click for more information on the human Mapping 100K set, or the 10K set). Click to learn about Affymetrix GeneChipĀ® Operating Software (GCOS) and GeneChipĀ® DNA Analysis Software (GDAS).
  • Affymetrix CNAT Affymetrix offers a Copy Number Analysis Tool (CNAT); learn more about it here. SNPscan substantially expands the ability to visualize and analyze data following the use of CNAT.
  • Affymetrix UCSC Genome Browser Affymetrix offers the ability to visualize a limited amount of SNP data on the UCSC Genome Browser; visit here (registration required).
  • dChipSNP From Cheng Li's group at Harvard. Significance curve and clustering of SNP array-based paired LOH data. Click here for the user's manual, or see publications by Lin et al. (2004)(PubMed).
  • CNAG From Seishi Ogawa's Group at the University of Tokyo. Nannya et al. (2005)(PubMed) described the Copy Number Analyzer for Affymetrix GeneChip Mapping 100K arrays (CNAG).
  • Haploblock HaploBlock is a software program which provides an integrated approach to haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution or reconstruction) and linkage disequilibrium (LD) mapping (or genetic association studies). HaploBlock is suitable for high density haplotype or genotype SNP marker data and is based on a statistical model which takes account of recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain at its core.