NanoStringQCPro

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Quality metrics and data processing methods for NanoString mRNA gene expression data

Bioconductor version: Release (3.17)

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 (from within R, enter citation("NanoStringQCPro")):

Installation

To install this package, start R (version "4.3") 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	PDF
Reference Manual	PDF
NEWS	Text

Details

biocViews	Microarray, Normalization, Preprocessing, QualityControl, ReportWriting, Software, mRNAMicroarray
Version	1.32.0
In Bioconductor since	BioC 3.1 (R-3.2) (8.5 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)
Linking To
Suggests	roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL

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	NanoStringQCPro_1.32.0.tar.gz
Windows Binary	NanoStringQCPro_1.31.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)	NanoStringQCPro_1.31.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NanoStringQCPro
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NanoStringQCPro
Package Short Url	https://bioconductor.org/packages/NanoStringQCPro/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive