ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions Public Deposited

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Creator
  • Ibrahim, Joseph
    • Affiliation: Gillings School of Global Public Health, Department of Biostatistics
  • Lieb, Jason D.
    • Affiliation: College of Arts and Sciences, Department of Biology, School of Medicine, Carolina Center for Genome Sciences, N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
  • Giresi, Paul G
    • Affiliation: College of Arts and Sciences, Department of Biology, School of Medicine, Carolina Center for Genome Sciences, N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
  • Rashid, Naim U
    • Affiliation: Gillings School of Global Public Health, Department of Biostatistics
  • Sun, Wei
    • Affiliation: School of Medicine, Department of Genetics, Gillings School of Global Public Health, Department of Biostatistics
Abstract
  • Abstract ZINBA (Zero-Inflated Negative Binomial Algorithm) identifies genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts. Software website: http://code.google.com/p/zinba/
Date of publication
Identifier
  • 21787385
  • doi:10.1186/gb-2011-12-7-r67
Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Naim U Rashid et al.; licensee BioMed Central Ltd.
License
Journal title
  • Genome Biology
Journal volume
  • 12
Journal issue
  • 7
Page start
  • R67
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1465-6906
Bibliographic citation
  • Genome Biology. 2011 Jul 25;12(7):R67
Access
  • Open Access
Publisher
  • BioMed Central Ltd