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

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 facto...

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Detalles Bibliográficos
Autores principales: Rashid, Naim U, Giresi, Paul G, Ibrahim, Joseph G, Sun, Wei, Lieb, Jason D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218829/
https://www.ncbi.nlm.nih.gov/pubmed/21787385
http://dx.doi.org/10.1186/gb-2011-12-7-r67
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author Rashid, Naim U
Giresi, Paul G
Ibrahim, Joseph G
Sun, Wei
Lieb, Jason D
author_facet Rashid, Naim U
Giresi, Paul G
Ibrahim, Joseph G
Sun, Wei
Lieb, Jason D
author_sort Rashid, Naim U
collection PubMed
description 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/
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spelling pubmed-32188292011-11-18 ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions Rashid, Naim U Giresi, Paul G Ibrahim, Joseph G Sun, Wei Lieb, Jason D Genome Biol Method 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/ BioMed Central 2011 2011-07-25 /pmc/articles/PMC3218829/ /pubmed/21787385 http://dx.doi.org/10.1186/gb-2011-12-7-r67 Text en Copyright ©2011 Rashid et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Rashid, Naim U
Giresi, Paul G
Ibrahim, Joseph G
Sun, Wei
Lieb, Jason D
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
title ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
title_full ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
title_fullStr ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
title_full_unstemmed ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
title_short ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
title_sort zinba integrates local covariates with dna-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218829/
https://www.ncbi.nlm.nih.gov/pubmed/21787385
http://dx.doi.org/10.1186/gb-2011-12-7-r67
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