oposSOM

This is the released version of oposSOM; for the devel version, see oposSOM.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

Comprehensive analysis of transcriptome data

Bioconductor version: Release (3.23)

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")):

Henry Loeffler-Wirth, Hoang Thanh Le and Martin Kalcher. oposSOM: Comprehensive analysis of transcriptome data. doi:10.18129/B9.bioc.oposSOM, R package version 2.30.0, https://bioconductor.org/packages/oposSOM.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, DifferentialExpression, GeneExpression, GeneSetEnrichment, Software, Visualization
Version	2.30.0
In Bioconductor since	BioC 3.0 (R-3.1) (12 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
System Requirements
URL	http://som.izbi.uni-leipzig.de

Suggests
Linking To	RcppParallel, Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	oposSOM_2.30.0.tar.gz
Windows Binary (x86_64)	oposSOM_2.30.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	oposSOM_2.30.0.tgz
macOS Binary (sonoma-arm64)	oposSOM_2.30.0.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/
Package Downloads Report	Download Stats