{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T03:27:52Z","timestamp":1778642872667,"version":"3.51.4"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase\u2013 or sonicated\u2013 ChIP-Seq data combined with either single-end or paired-end sequencing. PING uses a model-based approach, which enables nucleosome predictions even in the presence of low read counts. We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance with nucleR and ChIPseqR.<\/jats:p>\n               <jats:p>Availability: PING 2.0 is available from the Bioconductor website at http:\/\/bioconductor.org. It can run on Linux, Mac and Windows.<\/jats:p>\n               <jats:p>Contact: \u00a0rgottard@fhcrc.org<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary material is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt348","type":"journal-article","created":{"date-parts":[[2013,6,21]],"date-time":"2013-06-21T03:12:48Z","timestamp":1371784368000},"page":"2049-2050","source":"Crossref","is-referenced-by-count":16,"title":["PING 2.0: an R\/Bioconductor package for nucleosome positioning using next-generation sequencing data"],"prefix":"10.1093","volume":"29","author":[{"given":"Sangsoon","family":"Woo","sequence":"first","affiliation":[{"name":"1 Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA, 2Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA and 3Laboratory of Chromatin and Genomic Expression, Institut de Recherches Cliniques de Montreal, Montreal, QC H2W 1R7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuekui","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA, 2Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA and 3Laboratory of Chromatin and Genomic Expression, Institut de Recherches Cliniques de Montreal, Montreal, QC H2W 1R7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Renan","family":"Sauteraud","sequence":"additional","affiliation":[{"name":"1 Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA, 2Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA and 3Laboratory of Chromatin and Genomic Expression, Institut de Recherches Cliniques de Montreal, Montreal, QC H2W 1R7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fran\u00e7ois","family":"Robert","sequence":"additional","affiliation":[{"name":"1 Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA, 2Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA and 3Laboratory of Chromatin and Genomic Expression, Institut de Recherches Cliniques de Montreal, Montreal, QC H2W 1R7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raphael","family":"Gottardo","sequence":"additional","affiliation":[{"name":"1 Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA, 2Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA and 3Laboratory of Chromatin and Genomic Expression, Institut de Recherches Cliniques de Montreal, 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