spqn

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

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

Spatial quantile normalization

Bioconductor version: Release (3.23)

The spqn package implements spatial quantile normalization (SpQN). This method was developed to remove a mean-correlation relationship in correlation matrices built from gene expression data. It can serve as pre-processing step prior to a co-expression analysis.

Author: Yi Wang [cre, aut], Kasper Daniel Hansen [aut]

Maintainer: Yi Wang <yiwangthu5 at gmail.com>

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

Yi Wang, Kasper Daniel Hansen. spqn: Spatial quantile normalization. doi:10.18129/B9.bioc.spqn, R package version 1.24.0, https://bioconductor.org/packages/spqn.

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("spqn")

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("spqn")

spqn User's Guide	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GraphAndNetwork, NetworkInference, Normalization, Software
Version	1.24.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	Artistic-2.0
Depends	R (>= 4.0), ggplot2, ggridges, SummarizedExperiment, BiocGenerics
Imports	graphics, stats, utils, matrixStats
System Requirements
URL	https://github.com/hansenlab/spqn
Bug Reports	https://github.com/hansenlab/spqn/issues

Suggests	BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	spqn_1.24.0.tar.gz
Windows Binary (x86_64)	spqn_1.24.0.zip
macOS Binary (big-sur-x86_64)	spqn_1.24.0.tgz
macOS Binary (sonoma-arm64)	spqn_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/spqn
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/spqn
Package Short Url	https://bioconductor.org/packages/spqn/
Package Downloads Report	Download Stats