ngsReports

DOI: 10.18129/B9.bioc.ngsReports    

Load FastqQC reports and other NGS related files

Bioconductor version: Release (3.13)

This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R. As well as parsing files, multiple plotting methods have been implemented for visualising the parsed data. Plots can be generated as static ggplot objects or interactive plotly objects.

Author: Steve Pederson [aut, cre], Christopher Ward [aut], Thu-Hien To [aut]

Maintainer: Steve Pederson <stephen.pederson.au at gmail.com>

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ngsReports")

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("ngsReports")

 

HTML	R Script	An Introduction To ngsReports
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	QualityControl, ReportWriting, Software
Version	1.8.1
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	file LICENSE
Depends	R (>= 4.0.0), BiocGenerics, ggplot2, tibble (>= 1.3.1)
Imports	Biostrings, checkmate, dplyr (>= 1.0.0), DT, forcats, ggdendro, grDevices (>= 3.6.0), grid, lifecycle, lubridate, methods, pander, plotly (>= 4.9.4), readr, reshape2, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo
LinkingTo
Suggests	BiocStyle, Cairo, knitr, testthat, truncnorm
SystemRequirements
Enhances
URL	https://github.com/steveped/ngsReports
BugReports	https://github.com/steveped/ngsReports/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	ngsReports_1.8.1.tar.gz
Windows Binary	ngsReports_1.8.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	ngsReports_1.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ngsReports
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ngsReports
Package Short Url	https://bioconductor.org/packages/ngsReports/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.13	Source Archive