- Home
- Bioconductor 3.5
- Software Packages
- ATACseqQC
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 |
| Reference Manual |
Details
| biocViews | Coverage, DNASeq, GeneRegulation, NucleosomePositioning, QualityControl, Sequencing, Software |
| Version | 1.0.5 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 years) |
| 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.
| Source Package | ATACseqQC_1.0.5.tar.gz |
| Windows Binary | ATACseqQC_1.0.5.zip |
| Mac OS X 10.11 (El Capitan) | ATACseqQC_1.0.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ATACseqQC |
| Package Short Url | http://bioconductor.org/packages/ATACseqQC/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
