ngsReports
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ngsReports.
Load FastqQC reports and other NGS related files
Bioconductor version: 3.16
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: Stephen Pederson [aut, cre], Christopher Ward [aut], Thu-Hien To [aut]
Maintainer: Stephen Pederson <stephen.pederson.au at gmail.com>
citation("ngsReports")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | QualityControl, ReportWriting, Software |
| Version | 2.0.3 |
| In Bioconductor since | BioC 3.9 (R-3.6) (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 (>= 1.0.0), DT, forcats, ggdendro, grDevices (>= 3.6.0), grid, lifecycle, lubridate, methods, pander, plotly (>= 4.9.4), readr, reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo |
| System Requirements | |
| URL | https://github.com/steveped/ngsReports |
| Bug Reports | https://github.com/steveped/ngsReports/issues |
See More
| Suggests | BiocStyle, Cairo, knitr, 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_2.0.3.tar.gz |
| Windows Binary | ngsReports_2.0.3.zip |
| macOS Binary (x86_64) | ngsReports_2.0.3.tgz |
| macOS Binary (arm64) | ngsReports_2.0.3.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 3.16 | Source Archive |