NTAP: for NimbleGen tiling array ChIP-chip data analysis.
CONCLUSIONS
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.


METHODS
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.
He
Kun
K
College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China. hekun78@gmail.com
Li
Xueyong
X
Zhou
Junli
J
Deng
Xing-Wang
XW
Zhao
Hongyu
H
Luo
Jingchu
J
D047369:Chromatin Immunoprecipitation / Q000379:methods*; D030541:Databases, Genetic; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software