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>
Citation (from within R, enter
citation("ChIPexoQual")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, Coverage, QualityControl, Sequencing, Software, Transcription, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 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 |
| 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_1.8.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChIPexoQual/ |
| Package Short Url | https://bioconductor.org/packages/ChIPexoQual/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |