ngsReports

This is the released version of ngsReports; for the devel version, see ngsReports.

Load FastqQC reports and other NGS related files

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DOI: 10.18129/B9.bioc.ngsReports

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0001-8197-3303 , 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 "4.5") 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")

An Introduction To ngsReports HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews QualityControl, ReportWriting, Software

Version 2.12.1

In Bioconductor since BioC 3.9 (R-3.6) (6.5 years)

License LGPL-3

Depends R (>= 4.2.0), BiocGenerics, ggplot2 (>= 4.0.0), 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), 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

Suggests BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ngsReports_2.12.1.tar.gz

Windows Binary (x86_64) ngsReports_2.11.0.zip (64-bit only)

macOS Binary (x86_64) ngsReports_2.12.0.tgz

macOS Binary (arm64) ngsReports_2.12.1.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 3.22 Source Archive