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PING

A flexible and powerful open-source package for nucleosome positioning using MNase-Seq data or MNase– or sonicated– ChIP-Seq data combined with either single-end (SE) or paired-end (PE) sequencing. PING uses a model-based approach, which enables nucleosome predictions even in the presence of low read counts. It is a major update of an early (unpublished) version of the software and includes a novel statistical framework for PE data, new functions for pre-processing and reading raw data, and better integration with other Bioconductor packages. The result is a complete framework for nucleosome positioning within Bioconductor that can handle sonicated and MNase protocols combined with either SE or PE sequencing.

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PING forum

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PING classification

PING specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
2.16.0
Requirements:
chipseq, IRanges, GenomicRanges

PING distribution

versioning

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No versioning.

PING support

Documentation

Maintainer

  • Ren Sauteraud <>

Credits

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Publications

Institution(s)

Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA; Laboratory of Chromatin and Genomic Expression, Institut de Recherches Cliniques de Montreal, Montreal, QC, Canada

Funding source(s)

NSERC Postdoctoral Fellowship; National Institutes of Health [R01 HG005692]

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