title: PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.
abstract: CONCLUSIONS
  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- or sonicated- 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.
  
  
  BACKGROUND
  PING 2.0 is available from the Bioconductor website at http://bioconductor.org. It can run on Linux, Mac and Windows.
authors.affiliation: Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA.
authors.forename: Sangsoon
authors.initials: S
authors.lastname: Woo
authors.forename: Xuekui
authors.initials: X
authors.lastname: Zhang
authors.forename: Renan
authors.initials: R
authors.lastname: Sauteraud
authors.forename: François
authors.initials: F
authors.lastname: Robert
authors.forename: Raphael
authors.initials: R
authors.lastname: Gottardo
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D009707:Nucleosomes / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D009707:Nucleosomes