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esATAC

This is the development version of esATAC; for the stable release version, see esATAC.

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


Bioconductor version: Development (3.19)

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 qq.com>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("esATAC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("esATAC")
esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ATACSeq, Alignment, Coverage, DNASeq, DNaseSeq, ImmunoOncology, Preprocessing, QualityControl, Sequencing, Software
Version 1.25.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3 | file LICENSE
Depends R (>= 4.0.0), Rsamtools, GenomicRanges, ShortRead, pipeFrame
Imports Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, magrittr, digest, BSgenome, AnnotationDbi, GenomicAlignments, GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr
System Requirements C++11
URL https://github.com/wzthu/esATAC
Bug Reports https://github.com/wzthu/esATAC/issues
See More
Suggests BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package esATAC_1.25.0.tar.gz
Windows Binary esATAC_1.25.0.zip
macOS Binary (x86_64) esATAC_1.25.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/esATAC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/esATAC
Bioc Package Browser https://code.bioconductor.org/browse/esATAC/
Package Short Url https://bioconductor.org/packages/esATAC/
Package Downloads Report Download Stats