esATAC：一个用于 ATAC-seq 数据分析的易用系统流程。
esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis.
机构信息
Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China.
出版信息
Bioinformatics. 2018 Aug 1;34(15):2664-2665. doi: 10.1093/bioinformatics/bty141.
SUMMARY
ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present 'esATAC', a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines and provides flexible interfaces for building customized pipelines.
AVAILABILITY AND IMPLEMENTATION
esATAC package is open source under the GPL-3.0 license. It is implemented in R and C++. Source code and binaries for Linux, MAC OS X and Windows are available through Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/esATAC.html).
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
ATAC-seq 技术正在迅速成为研究染色质可及性的主要实验方法之一。本文介绍了 esATAC，这是一个高度集成的、易于使用的 R/Bioconductor 包，用于系统的 ATAC-seq 数据分析。它涵盖了完整分析流程的基本步骤，包括原始数据处理、质量控制以及下游的统计分析，如峰调用、富集分析和转录因子足迹分析。esATAC 支持针对预设管道的单个命令行执行，并提供了用于构建自定义管道的灵活接口。
可用性和实现
esATAC 包是遵循 GPL-3.0 许可证的开源软件。它是用 R 和 C++编写的。适用于 Linux、MAC OS X 和 Windows 的源代码和二进制文件可通过 Bioconductor（https://www.bioconductor.org/packages/release/bioc/html/esATAC.html）获得。
补充信息
补充数据可在《生物信息学》在线获取。
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