NanoStringDiff
This is the released version of NanoStringDiff; for the devel version, see NanoStringDiff.
Differential Expression Analysis of NanoString nCounter Data
Bioconductor version: Release (3.23)
This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. NanoStrongDiff incorporate size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized.
Author: hong wang <hong.wang at uky.edu>, tingting zhai <tingting.zhai at uky.edu>, chi wang <chi.wang at uky.edu>
Maintainer: tingting zhai <tingting.zhai at uky.edu>,hong wang <hong.wang at uky.edu>
citation("NanoStringDiff")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NanoStringDiff")
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("NanoStringDiff")| NanoStringDiff Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, Normalization, Software |
| Version | 1.42.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | GPL |
| Depends | Biobase |
| Imports | matrixStats, methods, Rcpp |
| System Requirements | |
| URL |
See More
| Suggests | testthat, BiocStyle |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | NanoTube |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | NanoStringDiff_1.42.0.tar.gz |
| Windows Binary (x86_64) | NanoStringDiff_1.42.0.zip |
| macOS Binary (big-sur-x86_64) | NanoStringDiff_1.42.0.tgz |
| macOS Binary (sonoma-arm64) | NanoStringDiff_1.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NanoStringDiff |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NanoStringDiff |
| Bioc Package Browser | https://code.bioconductor.org/browse/NanoStringDiff/ |
| Package Short Url | https://bioconductor.org/packages/NanoStringDiff/ |
| Package Downloads Report | Download Stats |