PIQ specifications


Unique identifier OMICS_11371
Name PIQ
Alternative name Protein Interaction Quantification
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input of PIQ is one or more DNase-seq experiments, the genome sequence of the organism assayed and a list of motifs represented as position weight matrices (PWMs) that describe candidate TF binding sites.
Output data The output of PIQ is the probability of occupancy for each candidate binding site in the genome, along with aggregate TF-specific scores (e.g. metrics for TF-specific chromatin opening).
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes



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  • person_outline David Gifford <>

Publication for Protein Interaction Quantification

PIQ institution(s)
Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, Cambridge, MA, USA
PIQ funding source(s)
The authors acknowledge funding from The National Institutes of Health Common Fund 5UL1DE019581, RL1DE019021 and 5TL1EB008540; the Harvard Stem Cell Institute's Sternlicht Director's Fund award, and NIH grants 1U01HG007037 and 5P01NS055923.

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