qsmooth

This is the development version of qsmooth; for the stable release version, see qsmooth.

Smooth quantile normalization

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DOI: 10.18129/B9.bioc.qsmooth

Bioconductor version: Development (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] ORCID iD ORCID: 0000-0002-7858-0231 , Kwame Okrah [aut], Koen Van den Berge [ctb], Hector Corrada Bravo [aut] ORCID iD ORCID: 0000-0002-1255-4444 , Rafael Irizarry [aut] ORCID iD ORCID: 0000-0002-3944-4309

Maintainer: Stephanie C. Hicks <shicks19 at jhu.edu>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, Microarray, MultipleComparison, Normalization, Preprocessing, RNASeq, Sequencing, Software

Version 1.27.0

In Bioconductor since BioC 3.9 (R-3.6) (6.5 years)

License GPL-3

Depends R (>= 4.0)

Imports SummarizedExperiment, utils, sva, stats, methods, graphics, Hmisc

System Requirements

URL

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_1.27.0.tar.gz

Windows Binary (x86_64) qsmooth_1.27.0.zip

macOS Binary (x86_64) qsmooth_1.27.0.tgz

macOS Binary (arm64) qsmooth_1.27.0.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/

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