ngsReports

DOI: 10.18129/B9.bioc.ngsReports  

Load FastqQC reports and other NGS related files

Bioconductor version: Release (3.17)

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

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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	2.2.4
In Bioconductor since	BioC 3.9 (R-3.6) (4.5 years)
License	file LICENSE
Depends	R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.4.0), patchwork (>= 1.1.1), tibble (>= 1.3.1)
Imports	Biostrings, checkmate, dplyr (>= 1.1.0), DT, forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, pander, plotly (>= 4.9.4), readr, reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo
LinkingTo
Suggests	BiocStyle, Cairo, knitr, testthat, truncnorm
SystemRequirements
Enhances
URL	https://github.com/smped/ngsReports
BugReports	https://github.com/smped/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_2.2.4.tar.gz
Windows Binary	ngsReports_2.2.4.zip
macOS Binary (x86_64)	ngsReports_2.2.4.tgz
macOS Binary (arm64)	ngsReports_2.2.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ngsReports
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ngsReports
Bioc Package Browser	https://code.bioconductor.org/browse/ngsReports/
Package Short Url	https://bioconductor.org/packages/ngsReports/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive