Journal
BIOINFORMATICS
Volume 34, Issue 15, Pages 2664-2665Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bty141
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Funding
- National Science Foundation of China [31371341, 61773230, 61721003]
- Tsinghua University Initiative Scientific Research Program [20141081175]
- Open Research Fund of State Key Laboratory of Bioelectronics, Southeast University
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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 Cthornthorn. 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). Contact: xwwang@tsinghua.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
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