NanoTube

This is the released version of NanoTube; for the devel version, see NanoTube.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14

An Easy Pipeline for NanoString nCounter Data Analysis

Bioconductor version: Release (3.23)

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] ORCID: 0000-0003-3130-3613 , Caiden Lukan [ctb]

Maintainer: Caleb Class <cclass at butler.edu>

Citation (from within R, enter citation("NanoTube")):

Caleb Class. NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis. doi:10.18129/B9.bioc.NanoTube, R package version 1.18.0, https://bioconductor.org/packages/NanoTube.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

Analyzing NanoString nCounter Data with the NanoTube	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, QualityControl, Software
Version	1.18.0
In Bioconductor since	BioC 3.14 (R-4.1) (5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.1), Biobase, ggplot2, limma
Imports	fgsea, methods, reshape, stats, utils
System Requirements
URL

Suggests	grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	NanoTube_1.18.0.tar.gz
Windows Binary (x86_64)	NanoTube_1.18.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	NanoTube_1.18.0.tgz
macOS Binary (sonoma-arm64)	NanoTube_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NanoTube
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NanoTube
Package Short Url	https://bioconductor.org/packages/NanoTube/
Package Downloads Report	Download Stats