NanoStringQCPro
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see NanoStringQCPro.
Quality metrics and data processing methods for NanoString mRNA gene expression data
Bioconductor version: 3.9
NanoStringQCPro provides a set of quality metrics that can be used to assess the quality of NanoString mRNA gene expression data -- i.e. to identify outlier probes and outlier samples. It also provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and an easily sharable html quality control output.
Author: Dorothee Nickles <nickles.dorothee at gene.com>, Thomas Sandmann <sandmann.thomas at gene.com>, Robert Ziman <ziman.robert at gene.com>, Richard Bourgon <bourgon.richard at gene.com>
Maintainer: Robert Ziman <ziman.robert at gene.com>
citation("NanoStringQCPro")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NanoStringQCPro")
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("NanoStringQCPro")| vignetteNanoStringQCPro.pdf | |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Microarray, Normalization, Preprocessing, QualityControl, ReportWriting, Software, mRNAMicroarray |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2), methods |
| Imports | AnnotationDbi(>= 1.26.0), org.Hs.eg.db(>= 2.14.0), Biobase(>= 2.24.0), knitr (>= 1.12), NMF (>= 0.20.5), RColorBrewer (>= 1.0-5), png (>= 0.1-7) |
| System Requirements | |
| URL |
See More
| Suggests | roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown |
| 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 | NanoStringQCPro_1.16.0.tar.gz |
| Windows Binary | NanoStringQCPro_1.16.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | NanoStringQCPro_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NanoStringQCPro |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NanoStringQCPro |
| Bioc Package Browser | https://code.bioconductor.org/browse/NanoStringQCPro/ |
| Package Short Url | https://bioconductor.org/packages/NanoStringQCPro/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |