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oposSOM

This is the development version of oposSOM; for the stable release version, see oposSOM.

Comprehensive analysis of transcriptome data

Bioconductor version: Development (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DataRepresentation, DifferentialExpression, GeneExpression, GeneSetEnrichment, Software, Visualization
Version 2.19.0
In Bioconductor since BioC 3.0 (R-3.1) (9 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
Linking To RcppParallel, Rcpp
Suggests
System Requirements
Enhances
URL http://som.izbi.uni-leipzig.de
See More
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_2.19.0.tar.gz
Windows Binary oposSOM_2.19.0.zip
macOS Binary (x86_64) oposSOM_2.19.0.tgz
macOS Binary (arm64) oposSOM_2.19.0.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