spqn
Spatial quantile normalization
Bioconductor version: Release (3.20)
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("spqn")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, NetworkInference, Normalization, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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 |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spqn_1.18.0.tar.gz |
| Windows Binary (x86_64) | spqn_1.18.0.zip |
| macOS Binary (x86_64) | spqn_1.18.0.tgz |
| macOS Binary (arm64) | spqn_1.17.0.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 |