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Additional Information

Competing Interests

There are no competing interests to declare.

Author Contributions

Russell Y Neches conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper, wrote the software.

Phillip M Seitzer conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper, wrote and modified tools for benchmarking and testing the software.

Elizabeth G Wilbanks performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper, beta-tested early versions of software, provided detailed feedback.

Marc T Facciotti analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper, advised and inspired the project.

Grant Disclosures

The following grant information was disclosed by the authors:

DARPA award number HR0011-05-1-0057

Alfred P. Sloan Foundation grant to Jonathan Eisen

UC Davis startup funds for Marc Facciotti

Data Deposition

The following information was supplied regarding the deposition of related data:

Code and documentation:

https://github.com/ryneches/pique

Test dataset:

http://figshare.com/articles/A_ChIP-seq_test_dataset/98106

Funding

This project was funded by UC Davis startup funds to M.T.F., NSF Graduate Research Fellowship awarded to E.G.W. R.Y.N. was supported by DARPA award number HR0011-05-1-0057 to Simon Levin, and by an Alfred P. Sloan Foundation grant to Jonathan Eisen. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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