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 (from within R, enter 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 PDF
Reference Manual PDF
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
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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