DOI: 10.18129/B9.bioc.esATAC    

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

Bioconductor version: Release (3.7)

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, Huan Fang, Yanda Li, Xiaowo Wang

Maintainer: Zheng Wei <wzweizheng at>, Wei Zhang <w-zhang16 at>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


HTML R Script An Introduction to esATAC
PDF   Reference Manual
Text   NEWS


biocViews ATACSeq, Alignment, Coverage, DNASeq, DNaseSeq, Preprocessing, QualityControl, Sequencing, Software
Version 1.2.1
License GPL-3 | file LICENSE
Depends R (>= 3.5), Rsamtools, GenomicRanges, ShortRead
Imports Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, DiagrammeR, magrittr, digest, BSgenome, AnnotationDbi, GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2016, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocInstaller, motifmatchr
LinkingTo Rcpp
Suggests BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,, DiagrammeRsvg, testthat, webshot
SystemRequirements C++11
Depends On Me
Imports Me
Suggests Me
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Source Package esATAC_1.2.1.tar.gz
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Mac OS X 10.11 (El Capitan) esATAC_1.2.1.tgz
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