ChIPexoQual

This is the released version of ChIPexoQual; for the devel version, see ChIPexoQual.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

ChIPexoQual

Bioconductor version: Release (3.23)

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>

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

Rene Welch, Dongjun Chung, Sunduz Keles. ChIPexoQual: ChIPexoQual. doi:10.18129/B9.bioc.ChIPexoQual, R package version 1.36.0, https://bioconductor.org/packages/ChIPexoQual.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

Vignette Title	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, ChIPSeq, Coverage, QualityControl, Sequencing, Software, Transcription, Visualization
Version	1.36.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	GPL (>=2)
Depends	R (>= 3.5.0), GenomicAlignments (>= 1.45.1)
Imports	methods, utils, Seqinfo, stats, BiocParallel, GenomicRanges (>= 1.61.1), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 2.25.1), 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
System Requirements
URL	https:github.com/keleslab/ChIPexoQual
Bug Reports	https://github.com/welch16/ChIPexoQual/issues

Suggests	ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ChIPexoQual_1.36.0.tar.gz
Windows Binary (x86_64)	ChIPexoQual_1.36.0.zip
macOS Binary (big-sur-x86_64)	ChIPexoQual_1.36.0.tgz
macOS Binary (sonoma-arm64)	ChIPexoQual_1.36.0.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