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Information
| Unique identifier | OMICS_19502 |
|---|---|
| Name | NMF |
| Alternative name | Non-negative Matrix Factorization |
| Software type | Package/Module, Pipeline/Workflow |
| Interface | Command line interface |
| Restrictions to use | None |
| Operating system | Unix/Linux, Mac OS, Windows |
| Programming languages | R |
| License | GNU General Public License version 3.0 |
| Computer skills | Advanced |
| Version | 0.21.0 |
| Stability | Stable |
| Requirements |
methods, stats, RColorBrewer, grid, graphics, Biobase, utils, grDevices, ggplot2, RUnit, knitr, gridBase, cluster, corpcor, reshape2, foreach, xtable, fastICA, digest, doParallel, colorspace, R(≥3.0.0), devtools, pkgmaker(≥0.20), registry, rngtools(≥1.2.3), stringr(≥1.0.0), doMPI, bigmemory(≥4.2), synchronicity(≥1.3.2), bibtex, mail
|
| Maintained | Yes |
Versioning
No version available
Documentation
- Documentation: https://cran.r-project.org/web/packages/NMF/NMF.pdf
- Issues: http://github.com/renozao/NMF/issues
Maintainer
- person_outline Renaud Gaujoux
NMF citations
(31)Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis
[…] porus) to filter out potential false-positive hits. FISCoG enrichment in each fungal taxon was assessed using BLASTP. The enrichment heat map was produced using the “aheat map” function in R package “NMF” (). The cladogram of the included taxa was reconstructed using IQ-TREE, based on 29 proteins (longer than 50 aa) encoded by single-copy genes. The GO names and subcellular protein locations of th […]
Integrative genomic profiling of large cell neuroendocrine carcinomas reveals distinct subtypes of high grade neuroendocrine lung tumors
[…] :T, C:G > G:C, C:G > T:A, A:T > C:G, A:T > G:C, A:T > T:A) in their tri-nucleotides sequence context (16 combinations for each type of substitution). For extracting mutational signatures, we used the non-negative matrix factorization (NMF) algorithm developed by Lee et al. and implemented in the Welcome Trust Sanger Institute (WTSI) mutational signatures framework. […]
A Carcinogen induced mouse model recapitulates the molecular alterations of human muscle invasive bladder cancer
[…] Framework [] or mutSignatures, an in-house R-ported version the same framework. The contribution of mutational signatures to mutation catalogs detected in mouse or human genomes was determined using NMF [] or DeconstructSigs [], with overlapping results. The TCGA bladder cancer mutational catalog for supplementary figure was obtained from Alexandrov et al. []. […]
Functionality of Root Associated Bacteria along a Salt Marsh Primary Succession
[…] st.The strength of each functional trait associated with the bacterial isolates from different plant compartments, plant species and soil types were visualized by using heatmap (function aheatmap) in NMF package (; ). Prior to analysis, the normalized absorbance values were further standardized by using Z-scores. Pie charts were used to summarize the proportion of bacterial isolates from one of th […]
Integrative analysis of genomic and epigenomic regulation of the transcriptome in liver cancer
[…] NMF cluster analysis with standard “brunet” method and 50 iterations was employed to identify stable sample clusters using CNVcor and METcor genes, respectively. Number of clusters k was set to 2 to 5 […]
Bacterial communities 16S rDNA fingerprinting as a potential tracing tool for cultured seabass Dicentrarchus labrax
[…] erated in R applying the package “venndiagram”. Bacterial composition among fish farms was visualized in heat maps with the associated dendrograms produced at family and genus level with the package “NMF” in R. Family/genus displaying a relative abundance >1% in at least one fish farm were considered in the analysis. […]
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