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PEER is used by a number of recent publications and analyses. Examples include:
1000 Genomes project A map of human genome variation from population-scale sequencing (Nature, Oct. 2010)
MuTHER (Multiple Tissue Human Expression Resource) The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study (PLoS Genetics, Jan. 2011)
HapMap 3 (forthcoming)
Using PEER for your own work? We'd like to know about it, get in touch.