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.
Bioinformatics. 2018 Feb 15;34(4):672-674. doi: 10.1093/bioinformatics/btx623.
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.
Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html.
Supplementary data are available at Bioinformatics online.
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。
diffloop 作为一个 R/Bioconductor 包实现，可在 https://bioconductor.org/packages/release/bioc/html/diffloop.html 获得。
补充数据可在生物信息学在线获得。
