Journal Article

NTAP: for NimbleGen tiling array ChIP-chip data analysis

Kun He, Xueyong Li, Junli Zhou, Xing-Wang Deng, Hongyu Zhao and Jingchu Luo

in Bioinformatics

Volume 25, issue 14, pages 1838-1840
Published in print July 2009 | ISSN: 1367-4803
Published online May 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp320

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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@mail.cbi.pku.edu.cn; luojc@pku.edu.cn; hekun78@gmail.com

Journal Article.  1246 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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