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ngsReports

This is the development version of ngsReports; for the stable release version, see ngsReports.

Load FastqQC reports and other NGS related files


Bioconductor version: Development (3.20)

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>

Citation (from within R, enter citation("ngsReports")):

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("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")
An Introduction To ngsReports HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews QualityControl, ReportWriting, Software
Version 2.7.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License LGPL-3
Depends R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.5.0), patchwork (>= 1.1.1), tibble (>= 1.3.1)
Imports Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo
System Requirements
URL https://github.com/smped/ngsReports
Bug Reports https://github.com/smped/ngsReports/issues
See More
Suggests BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm
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 ngsReports_2.7.0.tar.gz
Windows Binary ngsReports_2.7.0.zip (64-bit only)
macOS Binary (x86_64) ngsReports_2.7.0.tgz
macOS Binary (arm64) ngsReports_2.7.0.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