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Protocols

oposSOM specifications

Information


Unique identifier OMICS_09070
Name oposSOM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.18.0
Stability Stable
Requirements
Biobase, biomaRt, R(>=3.0), fastICA, som, fdrtool, ape, arules, scatterplot3d, igraph(>=1.0.0), tsne, pixmap
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Henry Löffler-Wirth

Publications for oposSOM

oposSOM citations

 (10)
library_books

Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles

2017
PLoS One
PMCID: 5669448
PMID: 29099860
DOI: 10.1371/journal.pone.0187572

[…] seven spot clusters assigned with capital letters A-G, each showing a specific profile of PSF-values in the studied diseases (). The full report of PSF-SOM is available at [].It should be noted that oposSOM scales data individually, before drawing the expression portraits, but applies spot detection thresholds on the global summary map, using all of the datasets at once (). Hence, there may be in […]

library_books

The non coding RNA landscape of human hematopoiesis and leukemia

2017
Nat Commun
PMCID: 5550424
PMID: 28794406
DOI: 10.1038/s41467-017-00212-4

[…] s. For the Arraystar Human lncRNA Microarray V2.0 and NCode Human Long Non-coding RNA microarray SOMs we used 17,655 and 14,256 ROSE-selected probes (mRNAs and ncRNAs), respectively, as inputs to the oposSOM package. The algorithm was run with the groupmap parameter set to 0.85; otherwise the default parameters recommended in the package vignette were used. The phylogenetic trees were reconstructe […]

call_split

Mapping heterogeneity in patient derived melanoma cultures by single cell RNA seq

2016
Oncotarget
PMCID: 5352202
PMID: 27903987
DOI: 10.18632/oncotarget.13666
call_split See protocol

[…] eviously []. For estimation of the quality of sample clustering we made use of the silhouette-plot []. All downstream methods have been described previously [, ] and are implemented in the R-package ‘oposSOM’ [].In order to demonstrate the similarity of replicate samples, a t-distributed stochastic neighbour embedding analysis (tSNE) []) was performed. The R-package ‘Seurat’ was used for running t […]

library_books

Single‐cell sequencing maps gene expression to mutational phylogenies in PDGF‐ and EGF‐driven gliomas

2016
Mol Syst Biol
PMCID: 5147052
PMID: 27888226
DOI: 10.15252/msb.20166969

[…] urther analysis. Pathway analysis was done using Pathway Commons (Cerami et al, ) via WEBGESTALT (Wang et al, ), and DAVID (Huang et al, ), transcription factor motif enrichment analysis was done via OPOSSOM (Sui Ho et al, ). Network interactions were computed via GeneMANIA (Montojo et al, ). […]

library_books

Genome wide DNA promoter methylation and transcriptome analysis in human adipose tissue unravels novel candidate genes for obesity

2016
PMCID: 5220399
PMID: 28123940
DOI: 10.1016/j.molmet.2016.11.003

[…] lized before downstream analysis. Expression data were then matched to methylation data and ranked by using the Mann–Whitney U test. Differential expression analysis was performed using the R package oposSOM . Results were listed as log fold change (logFC; , ). Differential expression and methylation were then analyzed together to identify genes being either up- or down-regulated and either hyper- […]

call_split

Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor Infiltrating T Regulatory Cells

2016
Immunity
PMCID: 5119953
PMID: 27851914
DOI: 10.1016/j.immuni.2016.10.021
call_split See protocol

[…] SOM analyses were carried out using the R package oposSOM using default parameters. Expression values of genes selected in the previous differential expression step were Z-score normalized and supplied in input to the automated pipeline for SOM train […]

Citations

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oposSOM institution(s)
Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany

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