EsATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis

Abstract

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.

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• http://dx.doi.org/10.1093/bioinformatics/bty141 under the license https://creativecommons.org/licenses/by-nc

• http://europepmc.org/articles/PMC6061683 under the license http://creativecommons.org/licenses/by-nc/4.0

• https://academic.oup.com/bioinformatics/article-pdf/34/15/2664/25230867/bty141.pdf

• http://academic.oup.com/bioinformatics/article-pdf/34/15/2664/25230867/bty141.pdf,

http://dx.doi.org/10.1093/bioinformatics/bty141 under the license cc-by-nc

• https://academic.oup.com/bioinformatics/article/34/15/2664/4924216,

https://pubmed.ncbi.nlm.nih.gov/29522192,

https://dblp.uni-trier.de/db/journals/bioinformatics/bioinformatics34.html#WeiZFLW18,

https://www.ncbi.nlm.nih.gov/pubmed/29522192,

https://academic.microsoft.com/#/detail/2792006949 under the license http://creativecommons.org/licenses/by-nc/4.0/