oposSOM

DOI: 10.18129/B9.bioc.oposSOM  

Comprehensive analysis of transcriptome data

Bioconductor version: Release (3.16)

This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.

Author: Henry Loeffler-Wirth <wirth at izbi.uni-leipzig.de>, Hoang Thanh Le <le at izbi.uni-leipzig.de> and Martin Kalcher <mkalcher at porkbox.net>

Maintainer: Henry Loeffler-Wirth <wirth at izbi.uni-leipzig.de>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("oposSOM")

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("oposSOM")

 

PDF	R Script	The oposSOM users guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, DifferentialExpression, GeneExpression, GeneSetEnrichment, Software, Visualization
Version	2.16.0
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 years)
License	GPL (>=2)
Depends	R (>= 4.0.0), igraph (>= 1.0.0)
Imports	fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt, Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl
LinkingTo	RcppParallel, Rcpp
Suggests
SystemRequirements
Enhances
URL	http://som.izbi.uni-leipzig.de
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	oposSOM_2.16.0.tar.gz
Windows Binary	oposSOM_2.16.0.zip
macOS Binary (x86_64)	oposSOM_2.16.0.tgz
macOS Binary (arm64)	oposSOM_2.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/oposSOM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/oposSOM
Bioc Package Browser	https://code.bioconductor.org/browse/oposSOM/
Package Short Url	https://bioconductor.org/packages/oposSOM/
Package Downloads Report	Download Stats