oposSOM

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see oposSOM.

Comprehensive analysis of transciptome data


Bioconductor version: 3.7

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> 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 "3.5") 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")
The oposSOM users guide PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataRepresentation, DifferentialExpression, GeneExpression, GeneSetEnrichment, Software, Visualization
Version 1.18.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL (>=2)
Depends R (>= 3.0), igraph (>= 1.0.0)
Imports som, fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt, Biobase, arules
System Requirements
URL http://som.izbi.uni-leipzig.de
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Package Archives

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

Source Package oposSOM_1.18.0.tar.gz
Windows Binary oposSOM_1.18.0.zip
Mac OS X 10.11 (El Capitan) oposSOM_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/oposSOM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/oposSOM
Package Short Url https://bioconductor.org/packages/oposSOM/
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Old Source Packages for BioC 3.7 Source Archive