Skip Navigation



Bioinformatics Advance Access published online on May 25, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp320
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
25/14/1838    most recent
btp320v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by He, K.
Right arrow Articles by Luo, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by He, K.
Right arrow Articles by Luo, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

NTAP: For NimbleGen Tiling Array ChIP-chip Data Analysis

Kun He 1,4,*, Xueyong Li 2,5, Junli Zhou 2,6, Xing-Wang Deng 2, Hongyu Zhao 3 and Jingchu Luo 1,*

1College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China
2Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
3Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520, USA
4Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, USA
5Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
6Beijing Kaituo DNA Biotech Research Center CO., Ltd., 39 West Shangdi Rd, Haidian District, Beijing 100085, China

*To whom correspondence should be addressed. Prof. Jingchu Luo, E-mail: luojc{at}mail.cbi.pku.edu.cn


  Abstract

Summary: NTAP is designed to analyze ChIP-chip data generated by the NimbleGen tiling array platform and to accomplish various pattern recognition tasks that are useful especially for epigenetic studies. The modular design of NTAP makes the data processing highly customizable. Users can either use NTAP to perform the full process of NimbleGen tiling array data analysis, or choose post-processing modules in NTAP to analyze pre-processed epigenetic data generated by other platforms. The output of NTAP can be saved in standard GFF format files and visualized in GBrowse.

Availability and Implementation: The source code of NTAP is freely available at http://ntap.cbi.pku.edu.cn/. It is implemented in Perl and R and can be used on Linux, Mac, and Windows platforms.

Contact: ntap{at}mail.cbi.pku.edu.cn

Associate Editor: Prof. John Quackenbush

Received on January 24, 2009; revised on May 10, 2009; accepted on May 12, 2009

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.