DOI: 10.18129/B9.bioc.oposSOM  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see oposSOM.

Comprehensive analysis of transcriptome data

Bioconductor version: 3.17

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")):


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if (!require("BiocManager", quietly = TRUE))


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


biocViews DataRepresentation, DifferentialExpression, GeneExpression, GeneSetEnrichment, Software, Visualization
Version 2.18.0
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
LinkingTo RcppParallel, Rcpp
URL http://som.izbi.uni-leipzig.de
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

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

Source Package oposSOM_2.18.0.tar.gz
Windows Binary oposSOM_2.18.0.zip
macOS Binary (x86_64) oposSOM_2.18.0.tgz
macOS Binary (arm64) oposSOM_2.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/oposSOM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/oposSOM
Bioc Package Browser https://code.bioconductor.org/browse/oposSOM/
Package Short Url https://bioconductor.org/packages/oposSOM/
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