wzthu/ATACFlow: An Easy-to-use Systematic pipeline for ATACseq data analysis

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.

Getting started

Package details

AuthorZheng Wei, Wei Zhang
Bioconductor views ATACSeq Alignment Coverage DNASeq DNaseSeq ImmunoOncology Preprocessing QualityControl Sequencing SingleCell
MaintainerZheng Wei <wzweizheng@qq.com>
LicenseGPL-3 | file LICENSE
URL https://github.com/wzthu/esATAC
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.