ngsReports

DOI: 10.18129/B9.bioc.ngsReports    

This is the development version of ngsReports; to use it, please install the devel version of Bioconductor.

Load FastqQC reports and other NGS related files

Bioconductor version: Development (3.10)

This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R, as well as visualising the data loaded from these files.

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

Maintainer: Steve Pederson <stephen.pederson at adelaide.edu.au>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews QualityControl, ReportWriting, Software
Version 1.1.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License LGPL (>= 3)
Depends BiocGenerics, ggplot2, tibble (>= 1.3.1)
Imports Biostrings, checkmate, dplyr (>= 0.7.5), ggdendro, grDevices, grid, lubridate, methods, parallel, plotly, readr, reshape2, rmarkdown, Rsamtools, scales, ShortRead, stats, stringr, tidyr, tidyselect (>= 0.2.3), truncnorm, utils, viridisLite, XVector, zoo
LinkingTo
Suggests BiocStyle, Cairo, knitr, pander, testthat
SystemRequirements
Enhances
URL https://github.com/UofABioinformaticsHub/ngsReports
BugReports https://github.com/UofABioinformaticsHub/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_1.1.0.tar.gz
Windows Binary ngsReports_1.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) ngsReports_1.1.0.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 http://bioconductor.org/packages/ngsReports/
Package Downloads Report Download Stats

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