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Protocols

NMF specifications

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


Maintainer


  • person_outline Renaud Gaujoux

NMF citations

 (31)
library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] 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 […]

library_books

Integrative genomic profiling of large cell neuroendocrine carcinomas reveals distinct subtypes of high grade neuroendocrine lung tumors

2018
Nat Commun
PMCID: 5849599
PMID: 29535388
DOI: 10.1038/s41467-018-03099-x

[…] :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. […]

library_books

A Carcinogen induced mouse model recapitulates the molecular alterations of human muscle invasive bladder cancer

2018
Oncogene
PMCID: 5886988
PMID: 29367767
DOI: 10.1038/s41388-017-0099-6

[…] 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. []. […]

library_books

Functionality of Root Associated Bacteria along a Salt Marsh Primary Succession

2017
Front Microbiol
PMCID: 5670159
PMID: 29163397
DOI: 10.3389/fmicb.2017.02102

[…] 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 […]

library_books

Integrative analysis of genomic and epigenomic regulation of the transcriptome in liver cancer

2017
Nat Commun
PMCID: 5635060
PMID: 29018224
DOI: 10.1038/s41467-017-00991-w

[…] 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 […]

library_books

Bacterial communities 16S rDNA fingerprinting as a potential tracing tool for cultured seabass Dicentrarchus labrax

2017
Sci Rep
PMCID: 5605529
PMID: 28928412
DOI: 10.1038/s41598-017-11552-y

[…] 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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