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.

Document type: Article

== Full document ==
<pdf>Media:Draft_Content_487521149-beopen1247-6956-document.pdf</pdf>


== Original document ==

The different versions of the original document can be found in:

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

* [http://europepmc.org/articles/PMC6061683 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 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://academic.oup.com/bioinformatics/article-pdf/34/15/2664/25230867/bty141.pdf],
: [http://dx.doi.org/10.1093/bioinformatics/bty141 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://academic.oup.com/bioinformatics/article/34/15/2664/4924216],
: [https://pubmed.ncbi.nlm.nih.gov/29522192 https://pubmed.ncbi.nlm.nih.gov/29522192],
: [https://dblp.uni-trier.de/db/journals/bioinformatics/bioinformatics34.html#WeiZFLW18 https://dblp.uni-trier.de/db/journals/bioinformatics/bioinformatics34.html#WeiZFLW18],
: [https://www.ncbi.nlm.nih.gov/pubmed/29522192 https://www.ncbi.nlm.nih.gov/pubmed/29522192],
: [https://academic.microsoft.com/#/detail/2792006949 https://academic.microsoft.com/#/detail/2792006949] under the license http://creativecommons.org/licenses/by-nc/4.0/