biosvd specifications


Unique identifier OMICS_15856
Name biosvd
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.16.0
Stability Stable
methods, grid, graphics, BiocGenerics, Biobase, R(>=3.1.0), NMF
Maintained Yes




No version available



  • person_outline Anneleen Daemen

biosvd citations


Non monotonic Changes in Progenitor Cell Behavior and Gene Expression during Aging of the Adult V SVZ Neural Stem Cell Niche

Stem Cell Reports
PMCID: 5785674
PMID: 29129683
DOI: 10.1016/j.stemcr.2017.10.005

[…] roup significantly changing genes based on similarity between their temporal expression patterns. Fuzzy clustering was conducted using the Mfuzz Bioconductor package for R. SVD was computed using the BioSVD Bioconductor package for R. We used GOSeq to identify the enriched GO categories of the total significantly changing genes. Treemaps were constructed using REVIGO. Max and min genes were termed […]


Integrated network analysis and logistic regression modeling identify stage specific genes in Oral Squamous Cell Carcinoma

BMC Med Genomics
PMCID: 4502639
PMID: 26179909
DOI: 10.1186/s12920-015-0114-0

[…] e first two principal components. In addition, hierarchical clustering was performed using gplots software package. Ward’s method with the Euclidean distance metric was used for the clustering.In the biosvd [] software package, the merged dataset was subjected to filtering out of eigengenes and eigenarrays—that were assumed to represent noise—by measuring steady-state gene expression and steady-sc […]

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