esATAC
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see esATAC.
An Easy-to-use Systematic pipeline for ATACseq data analysis
Bioconductor version: 3.7
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, Huan Fang, Yanda Li, Xiaowo Wang
Maintainer: Zheng Wei <wzweizheng at qq.com>, Wei Zhang <w-zhang16 at mails.tsinghua.edu.cn>
citation("esATAC")):
Installation
To install this package, start R (version "3.5") 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")| An Introduction to esATAC | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ATACSeq, Alignment, Coverage, DNASeq, DNaseSeq, Preprocessing, QualityControl, Sequencing, Software |
| Version | 1.2.3 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| 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, BiocInstaller, 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, DiagrammeRsvg, testthat, webshot |
| 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_1.2.3.tar.gz |
| Windows Binary | esATAC_1.2.3.zip (64-bit only) |
| Mac OS X 10.11 (El Capitan) | esATAC_1.2.3.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 |
| Old Source Packages for BioC 3.7 | Source Archive |