NanoTube

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see NanoTube.

An Easy Pipeline for NanoString nCounter Data Analysis

Bioconductor version: 3.14

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]

Maintainer: Caleb Class <cclass at butler.edu>

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

Installation

To install this package, start R (version "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneExpression, QualityControl, Software

Version 1.0.0

In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)

License GPL-3

Depends R (>= 4.1), Biobase, ggplot2

Imports fgsea, limma, methods, reshape, stats, utils

System Requirements

URL

Suggests grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, qusage, shiny, testthat, xlsx

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package NanoTube_1.0.0.tar.gz

Windows Binary NanoTube_1.0.0.zip

macOS 10.13 (High Sierra) NanoTube_1.0.0.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

Old Source Packages for BioC 3.14 Source Archive