An integrated software system for analyzing ChIP-chip and ChIP-seq data

被引：0

作者：

Hongkai Ji

Hui Jiang

Wenxiu Ma

David S Johnson

Richard M Myers

Wing H Wong

机构：

[1] Johns Hopkins Bloomberg School of Public Health,Department of Biostatistics

[2] Institute for Computational and Mathematical Engineering,Department of Computer Science

[3] Stanford University,Department of Genetics

[4] Stanford University,Department of Statistics

[5] Stanford University School of Medicine,Department of Health Research and Policy

[6] HudsonAlpha Institute for Biotechnology,undefined

[7] Stanford University,undefined

[8] Stanford University,undefined

[9] Present address: Gene Security Network,undefined

[10] Inc.,undefined

[11] 1442 Cortland Avenue,undefined

[12] San Francisco,undefined

[13] California 94110,undefined

[14] USA.,undefined

来源：

Nature Biotechnology | 2008年 / 26卷

关键词：

D O I：

暂无

中图分类号：

学科分类号：

摘要：

Analyzing the massive and heterogenous datasets from genome-wide chromatin immunoprecipitation (ChIP) datasets presents several computational and statistical challenges. Ji et al. present a software suite that integrates all steps in ChIP-chip and ChIP-seq data analyses and illustrate the use of these tools by comparing the ability of the two platforms to identify transcription factor binding sites.

引用

页码：1293 / 1300

页数：7

共 50 条

[41] BayesPeak: Bayesian analysis of ChIP-seq data
Spyrou, Christiana
Stark, Rory
Lynch, Andy G.
Tavare, Simon
BMC BIOINFORMATICS, 2009, 10 : 299
[42] ChIP-Enrich: gene set enrichment testing for ChIP-seq data
Welch, Ryan P.
Lee, Chee
Imbriano, Paul M.
Patil, Snehal
Weymouth, Terry E.
Smith, R. Alex
Scott, Laura J.
Sartor, Maureen A.
NUCLEIC ACIDS RESEARCH, 2014, 42 (13) : e105
[43] BayesPeak: Bayesian analysis of ChIP-seq data
Christiana Spyrou
Rory Stark
Andy G Lynch
Simon Tavaré
BMC Bioinformatics, 10
[44] A Statistical Framework for the Analysis of ChIP-Seq Data
Kuan, Pei Fen
Chung, Dongjun
Pan, Guangjin
Thomson, James A.
Stewart, Ron
Keles, Suenduez
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 2011, 106 (495) : 891 - 903
[45] Normalization and experimental design for ChIP-chip data
Peng, Shouyong
Alekseyenko, Artyom A.
Larschan, Erica
Kuroda, Mitzi I.
Park, Peter J.
BMC BIOINFORMATICS, 2007, 8 (1)
[46] Processing and analyzing ChIP-seq data: from short reads to regulatory interactions
Leleu, Marion
Lefebvre, Gregory
Rougemont, Jacques
BRIEFINGS IN FUNCTIONAL GENOMICS, 2010, 9 (5-6) : 466 - 476
[47] Normalization and experimental design for ChIP-chip data
Shouyong Peng
Artyom A Alekseyenko
Erica Larschan
Mitzi I Kuroda
Peter J Park
BMC Bioinformatics, 8
[48] rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments
Droit, Arnaud
Cheung, Charles
Gottardo, Raphael
BIOINFORMATICS, 2010, 26 (05) : 678 - 679
[49] Analysis of Controls in ChIP-seq
Awdeh, Aseel
Perkins, Theodore J.
ACM-BCB' 2017: PROCEEDINGS OF THE 8TH ACM INTERNATIONAL CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY,AND HEALTH INFORMATICS, 2017, : 620 - 620
[50] Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts
Toedling, Joern
Sklyar, Oleg
Huber, Wolfgang
BMC BIOINFORMATICS, 2007, 8 (1)

← 1 2 3 4 5 →