Bioconductor – esATAC

DOI: 10.18129/B9.bioc.esATAC  


This package is for version 3.12 of Bioconductor;
for the stable, up-to-date release version, see

An Easy-to-use Systematic pipeline for ATACseq data analysis

Bioconductor version: 3.12

This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.

Author: Zheng Wei, Wei Zhang

Maintainer: Zheng Wei <wzweizheng at>

Citation (from within R,
enter citation("esATAC")):


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“4.0”) and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


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esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis
PDF   Reference Manual
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biocViews ATACSeq, Alignment, Coverage, DNASeq, DNaseSeq, ImmunoOncology, Preprocessing, QualityControl, Sequencing, Software
Version 1.12.0
In Bioconductor since BioC 3.6 (R-3.4) (3.5 years)
License GPL-3 | file LICENSE
Depends R (>= 3.5), Rsamtools, GenomicRanges, ShortRead, pipeFrame
Imports Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, magrittr, digest, BSgenome, AnnotationDbi, GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr
LinkingTo Rcpp
Suggests BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,, testthat, webshot
SystemRequirements C++11
Depends On Me
Imports Me
Suggests Me
Links To Me
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