qsmooth
This is the released version of qsmooth; for the devel version, see qsmooth.
Smooth quantile normalization
Bioconductor version: Release (3.23)
Smooth quantile normalization is a generalization of quantile normalization, which is average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.
Author: Stephanie C. Hicks [aut, cre]
, Kwame Okrah [aut], Koen Van den Berge [ctb], Hector Corrada Bravo [aut]
, Rafael Irizarry [aut]
Maintainer: Stephanie C. Hicks <shicks19 at jhu.edu>
citation("qsmooth")):
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("qsmooth")
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("qsmooth")| The qsmooth user's guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Microarray, MultipleComparison, Normalization, Preprocessing, RNASeq, Sequencing, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0) |
| Imports | SummarizedExperiment, utils, sva, stats, methods, graphics, Hmisc |
| System Requirements | |
| URL |
See More
| Suggests | bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | CleanUpRNAseq |
| Suggests Me | metamorphr |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | qsmooth_1.28.0.tar.gz |
| Windows Binary (x86_64) | qsmooth_1.28.0.zip |
| macOS Binary (big-sur-x86_64) | qsmooth_1.28.0.tgz |
| macOS Binary (sonoma-arm64) | qsmooth_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/qsmooth |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/qsmooth |
| Bioc Package Browser | https://code.bioconductor.org/browse/qsmooth/ |
| Package Short Url | https://bioconductor.org/packages/qsmooth/ |
| Package Downloads Report | Download Stats |