1–30 of 123
Welcome to  the discussion group for users and developers of the Irreproducible Discovery Rate (IDR) statistical framework used to threshold and analyze reproducibility of quantitative biological experiments such as ChIP-seq data.

IDR was used extensively in the analysis of ChIP-seq data from the ENCODE (Encyclopedia of DNA elements) consortium. It is part of the official ENCODE/modENCODE data standards.

The statistcal method was developed by Qunhua Li, Ben Brown, Haiyan Huang and Peter Bickel at U.C. Berkeley. See for the publication in Annals of Applied Statistics (Li et al. 2011) introducing the statistical framework. For an intuitive description of the IDR method and a description of the various plots generated by the IDR package read this IDR-101 document compiled by Qunhua Li.

The method was further adapted, tweaked and deployed for systematic analysis of ChIP-seq data by Anshul Kundaje and others as part of the ENCODE consortium. 

A manuscript detailing practical aspects of the IDR pipeline is in the works. A beta version of the pipeline is available at