To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ATACseqQC")

In most cases, you don't need to download the package archive at all.

ATACseqQC

 

   

ATAC-seq Quality Control

Bioconductor version: Release (3.5)

ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.

Author: Jianhong Ou, Jun Yu, Michelle Kelliher, Lucio Castilla, Nathan Lawson, Lihua Julie Zhu

Maintainer: Jianhong Ou <jianhong.ou at umassmed.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ATACseqQC")

Documentation

HTML R Script ATACseqQC Vignette
PDF   Reference Manual

Details

biocViews Coverage, DNASeq, GeneRegulation, NucleosomePositioning, QualityControl, Sequencing, Software
Version 1.0.3
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL (>= 2)
Depends R (>= 3.4), BiocGenerics, S4Vectors
Imports BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools, randomForest, rtracklayer, stats, stringr
LinkingTo
Suggests RUnit, BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, motifStack, MotifDb, trackViewer
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source ATACseqQC_1.0.3.tar.gz
Windows Binary ATACseqQC_1.0.3.zip
Mac OS X 10.11 (El Capitan) ATACseqQC_1.0.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ATACseqQC/tree/release-3.5
Package Short Url http://bioconductor.org/packages/ATACseqQC/
Package Downloads Report Download Stats

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