esATAC

DOI: 10.18129/B9.bioc.esATAC    

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

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("esATAC", version = "3.8")

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")

 

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

Details

biocViews ATACSeq, Alignment, Coverage, DNASeq, DNaseSeq, Preprocessing, QualityControl, Sequencing, Software
Version 1.4.0
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, BiocManager, motifmatchr
LinkingTo Rcpp
Suggests BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, DiagrammeRsvg, testthat, webshot
SystemRequirements C++11
Enhances
URL https://github.com/wzthu/esATAC
BugReports https://github.com/wzthu/esATAC/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package esATAC_1.4.0.tar.gz
Windows Binary esATAC_1.4.0.zip (64-bit only)
Mac OS X 10.11 (El Capitan) esATAC_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/esATAC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/esATAC
Package Short Url http://bioconductor.org/packages/esATAC/
Package Downloads Report Download Stats

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