ChIPexoQual
This is the development version of ChIPexoQual; for the stable release version, see ChIPexoQual.
ChIPexoQual
Bioconductor version: Development (3.20)
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 "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
NEWS | Text |
Details
biocViews | Alignment, ChIPSeq, Coverage, QualityControl, Sequencing, Software, Transcription, Visualization |
Version | 1.29.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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 | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | ChIPexoQual_1.29.0.tar.gz |
Windows Binary | ChIPexoQual_1.29.0.zip (64-bit only) |
macOS Binary (x86_64) | ChIPexoQual_1.29.0.tgz |
macOS Binary (arm64) | ChIPexoQual_1.29.0.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 |