PIQ specifications

Unique identifier:
OMICS_11371
Software type:
Package/Module
Restrictions to use:
None
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).
Programming languages:
R
Version:
1.3
Maintained:
Yes
Name:
Protein Interaction Quantification
Interface:
Command line interface
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.
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable

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PIQ distribution

download

PIQ support

Maintainer

  • David Gifford <>

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Credits

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Publications

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

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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