IDR2D identifies reproducible genomic interactions

Author(s)
Krismer, Konstantin; Guo, Yuchun; Gifford, David K
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Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/
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Abstract
Chromatin interaction data from protocols such as ChIA-PET, HiChIP and Hi-C provide valuable insights into genome organization and gene regulation, but can include spurious interactions that do not reflect underlying genome biology. We introduce an extension of the Irreproducible Discovery Rate (IDR) method called IDR2D that identifies replicable interactions shared by chromatin interaction experiments. IDR2D provides a principled set of interactions and eliminates artifacts from single experiments. The method is available as a Bioconductor package for the R community, as well as an online service at https://idr2d.mit.edu.
Date issued
2020-02
URI
https://hdl.handle.net/1721.1/128915
Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Department of Biological Engineering; Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Journal
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Citation
Krismer, Konstantin et al. "IDR2D identifies reproducible genomic interactions." Nucleic Acids Research 48, 6 (February 2020): e31. © 2020 The Author(s)
Version: Final published version
ISSN
0305-1048
1362-4962
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