NanoTube

DOI: 10.18129/B9.bioc.NanoTube  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see NanoTube.

An Easy Pipeline for NanoString nCounter Data Analysis

Bioconductor version: 3.16

NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.

Author: Caleb Class [cre, aut] , Caiden Lukan [ctb]

Maintainer: Caleb Class <cclass at butler.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("NanoTube")

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("NanoTube")

 

HTML	R Script	NanoTube Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, QualityControl, Software
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.1), Biobase, ggplot2, limma
Imports	fgsea, methods, reshape, stats, utils
LinkingTo
Suggests	grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx
SystemRequirements
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	NanoTube_1.4.0.tar.gz
Windows Binary	NanoTube_1.4.0.zip
macOS Binary (x86_64)	NanoTube_1.4.0.tgz
macOS Binary (arm64)	NanoTube_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NanoTube
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NanoTube
Bioc Package Browser	https://code.bioconductor.org/browse/NanoTube/
Package Short Url	https://bioconductor.org/packages/NanoTube/
Package Downloads Report	Download Stats