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ChIPexoQual

ChIPexoQual


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Alignment, ChIPSeq, Coverage, QualityControl, Sequencing, Software, Transcription, Visualization
Version 1.26.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL (>=2)
Depends R (>= 3.5.0), 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
System Requirements
URL https:github.com/keleslab/ChIPexoQual
Bug Reports https://github.com/welch16/ChIPexoQual/issues
See More
Suggests ChIPexoQualExample(>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

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

Source Package ChIPexoQual_1.26.0.tar.gz
Windows Binary ChIPexoQual_1.26.0.zip
macOS Binary (x86_64) ChIPexoQual_1.26.0.tgz
macOS Binary (arm64) ChIPexoQual_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChIPexoQual
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChIPexoQual
Bioc Package Browser https://code.bioconductor.org/browse/ChIPexoQual/
Package Short Url https://bioconductor.org/packages/ChIPexoQual/
Package Downloads Report Download Stats