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
esATAC.

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 qq.com>

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

Installation

To install this package, start R (version
“4.0”) and enter:

if (!requireNamespace("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 1.12.0
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, org.Hs.eg.db, testthat, webshot
SystemRequirements C++11
Enhances
URL github.com/wzthu/esATAC
BugReports github.com/wzthu/esATAC/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

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package in your R session.


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