oposSOM
oposSOM is a bioinformatics tool developed to address the challenges of comprehensively analyzing genome-wide molecular data. It employs a self-organizing maps (SOM) machine learning approach, referred to as 'high-dimensional data portraying,' to provide intuitive visualization at single-sample resolution, facilitate biomarker selection, enable functional information mining, and achieve highly granular stratification of sample classes. The method has been successfully applied in various studies, primarily utilizing transcriptome data but extending to other OMIC realms.
Topic
Microarray experiment;Gene expression
Detail
Operation: Formatting
Software interface: Command-line user interface,Library
Language: R
License: GNU General Public License, version 2
Cost: Free
Version name: 2.20.0
Credit: The Federal Ministry of Education and Research (BMBF), FKZ.
Input: -
Output: -
Contact: Henry Loeffler-Wirth wirth@izbi.uni-leipzig.de
Collection: -
Maturity: Stable
Publications
- oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor.
- Löffler-Wirth H, et al. oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. 2015; 31:3225-7. doi: 10.1093/bioinformatics/btv342
- https://doi.org/10.1093/bioinformatics/btv342
- PMID: 26063839
- PMC: -
Download and documentation
Source: http://bioconductor.org/packages/release/bioc/src/contrib/oposSOM_2.20.0.tar.gz
Documentation: http://bioconductor.org/packages/release/bioc/manuals/oposSOM/man/oposSOM.pdf
Home page: http://bioconductor.org/packages/release/bioc/html/oposSOM.html
Links: http://bioconductor.org/packages/release/bioc/vignettes/oposSOM/inst/doc/Vignette.pdf
Links: http://bioconductor.org/packages/release/bioc/vignettes/oposSOM/inst/doc/Vignette.R
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