esATAC

DOI: 10.18129/B9.bioc.esATAC  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	ATACSeq, Alignment, Coverage, DNASeq, DNaseSeq, ImmunoOncology, Preprocessing, QualityControl, Sequencing, Software
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 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
LinkingTo	Rcpp
Suggests	BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, 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_1.20.0.tar.gz
Windows Binary	esATAC_1.20.0.zip
macOS Binary (x86_64)	esATAC_1.20.0.tgz
macOS Binary (arm64)	esATAC_1.20.0.tgz
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