NanoStringQCPro

This package is for version 3.14 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

DOI: 10.18129/B9.bioc.NanoStringQCPro

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Microarray, Normalization, Preprocessing, QualityControl, ReportWriting, Software, mRNAMicroarray

Version 1.26.0

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

Suggests roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown

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Package Archives

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

Source Package NanoStringQCPro_1.26.0.tar.gz

Windows Binary NanoStringQCPro_1.26.0.zip (32- & 64-bit)

macOS 10.13 (High Sierra) NanoStringQCPro_1.26.0.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 3.14 Source Archive