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Title: BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates

 [1];  [1];  [2];  [3];
  1. Department of Statistics, Iowa State University, Ames, IA, USA
  2. Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
  3. Department of Statistics, Iowa State University, Ames, IA, USA, Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
Publication Date:
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
Grant/Contract Number:  
Resource Type:
Published Article
Journal Name:
Additional Journal Information:
Journal Name: Bioinformatics Journal Volume: 34 Journal Issue: 17; Journal ID: ISSN 1367-4803
Oxford University Press
Country of Publication:
United Kingdom

Citation Formats

Goren, Emily, Liu, Peng, Wang, Chao, Wang, Chong, and Birol, ed., Inanc. BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates. United Kingdom: N. p., 2018. Web. doi:10.1093/bioinformatics/bty227.
Goren, Emily, Liu, Peng, Wang, Chao, Wang, Chong, & Birol, ed., Inanc. BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates. United Kingdom.
Goren, Emily, Liu, Peng, Wang, Chao, Wang, Chong, and Birol, ed., Inanc. Thu . "BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates". United Kingdom.
title = {BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates},
author = {Goren, Emily and Liu, Peng and Wang, Chao and Wang, Chong and Birol, ed., Inanc},
abstractNote = {},
doi = {10.1093/bioinformatics/bty227},
journal = {Bioinformatics},
number = 17,
volume = 34,
place = {United Kingdom},
year = {2018},
month = {4}

Works referenced in this record:

PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data
journal, June 2014

Suz12 binds to silenced regions of the genomein a cell-type-specific manner
journal, July 2006

An improved Bonferroni procedure for multiple tests of significance
journal, January 1986

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data
journal, January 2013

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
journal, March 2015

Model-based Analysis of ChIP-Seq (MACS)
journal, January 2008

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly
journal, May 2014

  • Lun, Aaron T. L.; Smyth, Gordon K.
  • Nucleic Acids Research, Vol. 42, Issue 11
  • DOI: 10.1093/nar/gku351

Genome-wide survey by ChIP-seq reveals YY1 regulation of lincRNAs in skeletal myogenesis
journal, August 2013

Is this the right normalization? A diagnostic tool for ChIP-seq normalization
journal, May 2015

Joint modeling of ChIP-seq data via a Markov random field model
journal, October 2013

The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis: Pax5 function in pro-B and mature B cells
journal, June 2012

  • Revilla-i-Domingo, Roger; Bilic, Ivan; Vilagos, Bojan
  • The EMBO Journal, Vol. 31, Issue 14
  • DOI: 10.1038/emboj.2012.155

jMOSAiCS: joint analysis of multiple ChIP-seq datasets
journal, January 2013

Independent filtering increases detection power for high-throughput experiments
journal, May 2010

  • Bourgon, R.; Gentleman, R.; Huber, W.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 21
  • DOI: 10.1073/pnas.0914005107

Summarizing and correcting the GC content bias in high-throughput sequencing
journal, February 2012

  • Benjamini, Yuval; Speed, Terence P.
  • Nucleic Acids Research, Vol. 40, Issue 10
  • DOI: 10.1093/nar/gks001

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
journal, February 2010

  • Bullard, James H.; Purdom, Elizabeth; Hansen, Kasper D.
  • BMC Bioinformatics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2105-11-94

An integrated software system for analyzing ChIP-chip and ChIP-seq data
journal, November 2008

  • Ji, Hongkai; Jiang, Hui; Ma, Wenxiu
  • Nature Biotechnology, Vol. 26, Issue 11
  • DOI: 10.1038/nbt.1505

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
journal, January 2012

  • McCarthy, Davis J.; Chen, Yunshun; Smyth, Gordon K.
  • Nucleic Acids Research, Vol. 40, Issue 10
  • DOI: 10.1093/nar/gks042

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
journal, June 2009

Design and analysis of ChIP-seq experiments for DNA-binding proteins
journal, November 2008

  • Kharchenko, Peter V.; Tolstorukov, Michael Y.; Park, Peter J.
  • Nature Biotechnology, Vol. 26, Issue 12
  • DOI: 10.1038/nbt.1508

Measuring reproducibility of high-throughput experiments
journal, September 2011

  • Li, Qunhua; Brown, James B.; Huang, Haiyan
  • The Annals of Applied Statistics, Vol. 5, Issue 3
  • DOI: 10.1214/11-AOAS466

A Method for Selecting the Bin Size of a Time Histogram
journal, June 2007

Systematic evaluation of factors influencing ChIP-seq fidelity
journal, April 2012

  • Chen, Yiwen; Negre, Nicolas; Li, Qunhua
  • Nature Methods, Vol. 9, Issue 6
  • DOI: 10.1038/nmeth.1985

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
journal, August 2012

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
journal, May 2010

Leveraging Biological Replicates to Improve Analysis in Chip-Seq Experiments
journal, January 2014

  • Yang, Yajie; Fear, Justin; Hu, Jianhong
  • Computational and Structural Biotechnology Journal, Vol. 9, Issue 13
  • DOI: 10.5936/csbj.201401002

A Statistical Framework for the Analysis of ChIP-Seq Data
journal, September 2011

  • Kuan, Pei Fen; Chung, Dongjun; Pan, Guangjin
  • Journal of the American Statistical Association, Vol. 106, Issue 495
  • DOI: 10.1198/jasa.2011.ap09706

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering
journal, September 2016

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
journal, January 2009

Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates
journal, January 2012

  • Lund, Steven P.; Nettleton, Dan; McCarthy, Davis J.
  • Statistical Applications in Genetics and Molecular Biology, Vol. 11, Issue 5
  • DOI: 10.1515/1544-6115.1826

Species-Specific Strategies Underlying Conserved Functions of Metabolic Transcription Factors
journal, April 2011

  • Soccio, Raymond E.; Tuteja, Geetu; Everett, Logan J.
  • Molecular Endocrinology, Vol. 25, Issue 4
  • DOI: 10.1210/me.2010-0454

ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia
journal, November 2012

JAMM: a peak finder for joint analysis of NGS replicates
journal, September 2014

Uniform, optimal signal processing of mapped deep-sequencing data
journal, June 2013

  • Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul
  • Nature Biotechnology, Vol. 31, Issue 7
  • DOI: 10.1038/nbt.2596

Large-Scale Quality Analysis of Published ChIP-seq Data
journal, December 2013

  • Marinov, Georgi K.; Kundaje, Anshul; Park, Peter J.
  • G3: Genes|Genomes|Genetics, Vol. 4, Issue 2
  • DOI: 10.1534/g3.113.008680

Detecting differential binding of transcription factors with ChIP-seq
journal, November 2011

Mapping genome-wide transcription factor binding sites in frozen tissues
journal, January 2013

  • Savic, Daniel; Gertz, Jason; Jain, Preti
  • Epigenetics & Chromatin, Vol. 6, Issue 1
  • DOI: 10.1186/1756-8935-6-30

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
journal, September 2014

  • Meyer, Clifford A.; Liu, X. Shirley
  • Nature Reviews Genetics, Vol. 15, Issue 11
  • DOI: 10.1038/nrg3788

Genome-Wide Analysis of Chromatin States Reveals Distinct Mechanisms of Sex-Dependent Gene Regulation in Male and Female Mouse Liver
journal, July 2013

  • Sugathan, A.; Waxman, D. J.
  • Molecular and Cellular Biology, Vol. 33, Issue 18
  • DOI: 10.1128/MCB.00280-13

The Sequence Alignment/Map format and SAMtools
journal, June 2009

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
journal, January 1995

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
journal, September 2012

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates
journal, June 2013

Using combined evidence from replicates to evaluate ChIP-seq peaks
journal, May 2015