ChIPexoQual

DOI: 10.18129/B9.bioc.ChIPexoQual    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ChIPexoQual.

ChIPexoQual

Bioconductor version: 3.14

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")):

Installation

To install this package, start R (version "4.1") 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")

 

HTML R Script Vignette Title
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, ChIPSeq, Coverage, QualityControl, Sequencing, Software, Transcription, Visualization
Version 1.18.0
In Bioconductor since BioC 3.5 (R-3.4) (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_1.18.0.tar.gz
Windows Binary ChIPexoQual_1.18.0.zip
macOS 10.13 (High Sierra) ChIPexoQual_1.18.0.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/
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