spqn

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see spqn.

Spatial quantile normalization

Bioconductor version: 3.14

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")):

Installation

To install this package, start R (version "4.1") 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 1.6.0

In Bioconductor since BioC 3.11 (R-4.0) (4 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

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Build Report Build Report

Package Archives

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

Source Package spqn_1.6.0.tar.gz

Windows Binary spqn_1.6.0.zip

macOS 10.13 (High Sierra) spqn_1.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/spqn

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spqn

Bioc Package Browser https://code.bioconductor.org/browse/spqn/

Package Short Url https://bioconductor.org/packages/spqn/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive