ATACseqQC
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ATACseqQC.
ATAC-seq Quality Control
Bioconductor version: 3.9
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, Haibo Liu, Feng Yan, Jun Yu, Michelle Kelliher, Lucio Castilla, Nathan Lawson, Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou at duke.com>
citation("ATACseqQC")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ATACseqQC")
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("ATACseqQC")| ATACseqQC Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, Coverage, DNASeq, GeneRegulation, ImmunoOncology, NucleosomePositioning, QualityControl, Sequencing, Software |
| Version | 1.8.5 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.4), BiocGenerics, S4Vectors |
| Imports | BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools(>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | NADfinder |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ATACseqQC_1.8.5.tar.gz |
| Windows Binary | ATACseqQC_1.8.5.zip |
| Mac OS X 10.11 (El Capitan) | ATACseqQC_1.8.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ATACseqQC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ATACseqQC |
| Bioc Package Browser | https://code.bioconductor.org/browse/ATACseqQC/ |
| Package Short Url | https://bioconductor.org/packages/ATACseqQC/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |