ChIPexoQual

DOI: 10.18129/B9.bioc.ChIPexoQual    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ChIPexoQual.

ChIPexoQual

Bioconductor version: 3.9

Package with a quality control pipeline for ChIP-exo/nexus data.

Author: Rene Welch, Dongjun Chung, Sunduz Keles

Maintainer: Rene Welch <welch at stat.wisc.edu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChIPexoQual")

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("ChIPexoQual")

 

HTML	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, ChIPSeq, Coverage, QualityControl, Sequencing, Software, Transcription, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	GPL (>=2)
Depends	R (>= 3.4.0), GenomicAlignments(>= 1.0.1)
Imports	methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges(>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools(>= 1.16.1), IRanges(>= 1.6), S4Vectors(>= 0.8), biovizBase(>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown
LinkingTo
Suggests	ChIPexoQualExample(>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat
SystemRequirements
Enhances
URL	https:github.com/keleslab/ChIPexoQual
BugReports	https://github.com/welch16/ChIPexoQual/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ChIPexoQual_1.8.0.tar.gz
Windows Binary	ChIPexoQual_1.8.0.zip
Mac OS X 10.11 (El Capitan)	ChIPexoQual_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChIPexoQual
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChIPexoQual
Package Short Url	https://bioconductor.org/packages/ChIPexoQual/
Package Downloads Report	Download Stats