This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ChIPexoQual.
Bioconductor version: 3.13
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")
):
To install this package, start R (version "4.1") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("ChIPexoQual")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPexoQual")
HTML | R Script | Vignette Title |
Reference Manual | ||
Text | NEWS |
biocViews | Alignment, ChIPSeq, Coverage, QualityControl, Sequencing, Software, Transcription, Visualization |
Version | 1.16.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (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 |
Follow Installation instructions to use this package in your R session.
Source Package | ChIPexoQual_1.16.0.tar.gz |
Windows Binary | ChIPexoQual_1.16.0.zip |
macOS 10.13 (High Sierra) | ChIPexoQual_1.16.0.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 |
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