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NanoTube

An Easy Pipeline for NanoString nCounter Data Analysis


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
NanoTube Vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GeneExpression, QualityControl, Software
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.1), Biobase, ggplot2, limma
Imports fgsea, methods, reshape, stats, utils
System Requirements
URL
See More
Suggests grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

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

Source Package NanoTube_1.8.0.tar.gz
Windows Binary NanoTube_1.8.0.zip
macOS Binary (x86_64) NanoTube_1.8.0.tgz
macOS Binary (arm64) NanoTube_1.8.0.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