diffloop：一种从测序数据中识别和分析差异 DNA 环的计算框架。
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.
机构信息
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
出版信息
Bioinformatics. 2018 Feb 15;34(4):672-674. doi: 10.1093/bioinformatics/btx623.
SUMMARY
The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state.
AVAILABILITY AND IMPLEMENTATION
Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
细胞核内 DNA 的 3D 结构是基因、调控元件和转录机制之间相互作用的关键决定因素。因此，DNA 环化结构的差异与基因表达和细胞状态的变化有关。为了系统地评估样本间 DNA 环化结构的变化，我们引入了 diffloop，这是一个 R/Bioconductor 包，提供了一系列用于 DNA 环的质量控制、统计检验、注释和可视化的功能。我们通过检测 ENCODE ChIA-PET 样本之间的差异来证明这一功能，并将环化与表观遗传状态的可变性联系起来。
可用性和实现
diffloop 作为一个 R/Bioconductor 包实现，可在 https://bioconductor.org/packages/release/bioc/html/diffloop.html 获得。
联系方式
补充信息
补充数据可在生物信息学在线获得。
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