NTAP: for NimbleGen tiling array ChIP-chip data analysis

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 NT...

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Autores principales: He, Kun, Li, Xueyong, Zhou, Junli, Deng, Xing-Wang, Zhao, Hongyu, Luo, Jingchu
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705232/
https://www.ncbi.nlm.nih.gov/pubmed/19468055
http://dx.doi.org/10.1093/bioinformatics/btp320
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author He, Kun
Li, Xueyong
Zhou, Junli
Deng, Xing-Wang
Zhao, Hongyu
Luo, Jingchu
author_facet He, Kun
Li, Xueyong
Zhou, Junli
Deng, Xing-Wang
Zhao, Hongyu
Luo, Jingchu
author_sort He, Kun
collection PubMed
description 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
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spelling pubmed-27052322009-07-06 NTAP: for NimbleGen tiling array ChIP-chip data analysis He, Kun Li, Xueyong Zhou, Junli Deng, Xing-Wang Zhao, Hongyu Luo, Jingchu Bioinformatics Applications Note 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 Oxford University Press 2009-07-15 2009-05-25 /pmc/articles/PMC2705232/ /pubmed/19468055 http://dx.doi.org/10.1093/bioinformatics/btp320 Text en http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Applications Note
He, Kun
Li, Xueyong
Zhou, Junli
Deng, Xing-Wang
Zhao, Hongyu
Luo, Jingchu
NTAP: for NimbleGen tiling array ChIP-chip data analysis
title NTAP: for NimbleGen tiling array ChIP-chip data analysis
title_full NTAP: for NimbleGen tiling array ChIP-chip data analysis
title_fullStr NTAP: for NimbleGen tiling array ChIP-chip data analysis
title_full_unstemmed NTAP: for NimbleGen tiling array ChIP-chip data analysis
title_short NTAP: for NimbleGen tiling array ChIP-chip data analysis
title_sort ntap: for nimblegen tiling array chip-chip data analysis
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705232/
https://www.ncbi.nlm.nih.gov/pubmed/19468055
http://dx.doi.org/10.1093/bioinformatics/btp320
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AT luojingchu ntapfornimblegentilingarraychipchipdataanalysis

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