染色质开关：一种灵活的方法来检测染色质状态转换。
chromswitch: a flexible method to detect chromatin state switches.
机构信息
Department of Human Genetics, McGill University, Montreal, QC, Canada and Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada.
出版信息
Bioinformatics. 2018 Jul 1;34(13):2286-2288. doi: 10.1093/bioinformatics/bty075.
SUMMARY
Chromatin state plays a major role in controlling gene expression, and comparative analysis of ChIP-seq data is key to understanding epigenetic regulation. We present chromswitch, an R/Bioconductor package to integrate epigenomic data in a defined window of interest to detect an overall switch in chromatin state. Chromswitch accurately classifies a benchmarking dataset, and when applied genome-wide, the tool successfully detects chromatin changes that result in brain-specific expression.
AVAILABILITY AND IMPLEMENTATION
Chromswitch is implemented as an R package available from Bioconductor at https://bioconductor.org/packages/chromswitch. All data and code for reproducing the analysis presented in this paper are available at https://doi.org/10.5281/zenodo.1101260.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
染色质状态在控制基因表达中起着重要作用，比较分析 ChIP-seq 数据是理解表观遗传调控的关键。我们提出了 chromswitch，这是一个 R/Bioconductor 包，用于在感兴趣的定义窗口中整合组蛋白数据，以检测染色质状态的整体转换。Chromswitch 可以准确地对基准数据集进行分类，并且在全基因组范围内应用时，该工具可以成功检测导致大脑特异性表达的染色质变化。
可用性和实现
Chromswitch 作为一个 R 包实现，可从 Bioconductor 获得，网址为 https://bioconductor.org/packages/chromswitch。本文中呈现的分析的所有数据和代码都可在 https://doi.org/10.5281/zenodo.1101260 处获得。
补充信息
补充数据可在 Bioinformatics 在线获得。
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