Yu Guangchuang, Wang Li-Gen, He Qing-Yu
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632, China, State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China and.
Guangdong Information Center, Guangzhou 510031, China.
Bioinformatics. 2015 Jul 15;31(14):2382-3. doi: 10.1093/bioinformatics/btv145. Epub 2015 Mar 11.
ChIPseeker is an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions. Comparison of ChIP peak profiles and annotation are also supported. Moreover, it supports evaluating significant overlap among ChIP-seq datasets. Currently, ChIPseeker contains 15 000 bed file information from GEO database. These datasets can be downloaded and compare with user's own data to explore significant overlap datasets for inferring co-regulation or transcription factor complex for further investigation.
ChIPseeker is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html).
ChIPseeker是一个用于注释ChIP-seq数据分析的R包。它支持对ChIP峰进行注释，并提供可视化ChIP峰在染色体上的覆盖情况以及与转录起始位点（TSS）区域结合的峰的图谱的功能。还支持ChIP峰图谱和注释的比较。此外，它支持评估ChIP-seq数据集之间的显著重叠。目前，ChIPseeker包含来自GEO数据库的15000个bed文件信息。这些数据集可以下载并与用户自己的数据进行比较，以探索显著重叠的数据集，用于推断共调控或转录因子复合物以便进一步研究。
ChIPseeker根据Artistic-2.0许可发布。源代码和文档可通过Bioconductor（http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html）免费获取。
