quantro

This is the released version of quantro; for the devel version, see quantro.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

A test for when to use quantile normalization

Bioconductor version: Release (3.23)

A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.

Author: Stephanie Hicks [aut, cre] ORCID: 0000-0002-7858-0231 , Rafael Irizarry [aut] ORCID: 0000-0002-3944-4309

Maintainer: Stephanie Hicks <shicks19 at jhu.edu>

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

Stephanie Hicks, Rafael Irizarry. quantro: A test for when to use quantile normalization. doi:10.18129/B9.bioc.quantro, R package version 1.46.0, https://bioconductor.org/packages/quantro.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("quantro")

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("quantro")

The quantro user's guide	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Microarray, MultipleComparison, Normalization, Preprocessing, Sequencing, Software
Version	1.46.0
In Bioconductor since	BioC 3.0 (R-3.1) (12 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	Biobase, minfi, doParallel, foreach, iterators, ggplot2, methods, RColorBrewer
System Requirements
URL

Suggests	rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me	netZooR, yarn
Suggests Me	extraChIPs, qsmooth
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	quantro_1.46.0.tar.gz
Windows Binary (x86_64)	quantro_1.46.0.zip
macOS Binary (big-sur-x86_64)	quantro_1.46.0.tgz
macOS Binary (sonoma-arm64)	quantro_1.46.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/quantro
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/quantro
Package Short Url	https://bioconductor.org/packages/quantro/
Package Downloads Report	Download Stats