oposSOM
Comprehensive analysis of transcriptome data
Bioconductor version: Release (3.20)
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("oposSOM")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, DifferentialExpression, GeneExpression, GeneSetEnrichment, Software, Visualization |
| Version | 2.24.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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 |
See More
| Suggests | |
| Linking To | RcppParallel, Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | oposSOM_2.24.0.tar.gz |
| Windows Binary (x86_64) | oposSOM_2.24.0.zip |
| macOS Binary (x86_64) | oposSOM_2.24.0.tgz |
| macOS Binary (arm64) | oposSOM_2.24.0.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 |