ZINBA pipeline

ZINBA specifications

Information


Unique identifier OMICS_00465
Name ZINBA
Alternative name Zero-Inflated Negative Binomial Algorithm
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.02.03
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Jason Lieb <>
  • person_outline Wei Sun <>

Publication for Zero-Inflated Negative Binomial Algorithm

ZINBA citations

 (2)
2015
PMCID: 4575638

[…] reference, were removed., read alignment positions were adjusted according to their strand: +4 bp for + strand alignments, and −5 bp for − strand alignments. open chromatin regions were called using zinba53 with a window size of 300 bp, an offset of 75 bp, and a posterior probability threshold of 0.8., for nucleosome positioning, properly paired alignments were filtered by their fragment size. […]

2015
PMCID: 4362815

[…] was allowed to occur up to four times throughout the genome, where one was selected at random for each of those positions that were not unique. the set of enriched regions were then identified by zinba[26], using 300-bp windows with 75-bp offsets [see additional files 2 and 3]. the background and enriched components were modeled using g/c content and an interaction term between mapability […]

ZINBA institution(s)
Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics and School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
ZINBA funding source(s)
Supported by the NIH Biostatistics Training Grant in Cancer Genomics and NIH grants Bayesian Approaches to Model Selection for Survival Data (GM70335), Inference with Missing Covariates in Regression Models (CA74015), and ENCODE grant U54 HG004563.

ZINBA review

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Fabien Pichon

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Desktop
Too many files to generate for each experiment (very time consuming!) for a result far from satisfying.
To balance my comment, I have to say that I used ZINBA on FAIRE-seq which is relatively more noisy compared to ChIP-seq.
But another black point is that there is almost no support for a lot issues and instabilities.
For FAIRE-seq I would prefer Fseq and for ChIP-seq I would prefer MACS.