Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 8 committers (12.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.4%) to scientific vocabulary
Repository
NMF: A Flexible R package for Nonnegative Matrix Factorization
Basic Info
- Host: GitHub
- Owner: renozao
- Language: R
- Default Branch: master
- Size: 106 MB
Statistics
- Stars: 151
- Watchers: 15
- Forks: 42
- Open Issues: 125
- Releases: 0
Metadata Files
README.md
title: "NMF R package -- Algorithms and Framework for Nonnegative Matrix Factorization (NMF)"
Background
Nonnegative Matrix Factorization (NMF) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applications of NMF in bioinformatics have demonstrated its ability to extract meaningful information from high-dimensional data such as gene expression microarrays. Developments in NMF theory and applications have resulted in a variety of algorithms and methods. However, most NMF implementations have been on commercial platforms, while those that are freely available typically require programming skills. This limits their use by the wider research community.
Results
Our objective is to provide the bioinformatics community with an open-source, easy-to-use and unified interface to standard NMF algorithms, as well as with a simple framework to help implement and test new NMF methods. For that purpose, we have developed a package for the R/BioConductor platform. The package ports public code to R, and is structured to enable users to easily modify and/or add algorithms. It includes a number of published NMF algorithms and initialization methods and facilitates the combination of these to produce new NMF strategies. Commonly used benchmark data and visualization methods are provided to help in the comparison and interpretation of the results.
Conclusions
The NMF package helps realize the potential of Nonnegative Matrix Factorization, especially in bioinformatics, providing easy access to methods that have already yielded new insights in many applications.
Availability
Documentation, source code and sample data are available in different places:
Latest stable release from CRAN: https://cran.r-project.org/package=NMF
Development versions on Github:
- Stable: https://github.com/renozao/NMF@master
- Bleed-edge: https://github.com/renozao/NMF@devel
Travis check: 
Owner
- Name: Renaud Gaujoux
- Login: renozao
- Kind: user
- Location: Haifa, Israel
- Company: Systems Immunology & Precision Medicine, Technion
- Repositories: 20
- Profile: https://github.com/renozao
GitHub Events
Total
- Issues event: 5
- Watch event: 13
- Issue comment event: 6
- Fork event: 3
Last Year
- Issues event: 5
- Watch event: 13
- Issue comment event: 6
- Fork event: 3
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Renaud | r****d@t****l | 265 |
| renaud | r****d@e****b | 159 |
| Renaud | g****x@g****m | 93 |
| Renaud | r****o@u****m | 39 |
| Keith Hughitt | k****t@g****m | 2 |
| Jim Hester | j****r@g****m | 1 |
| Renaud | r****d@z****s | 1 |
| stefan7th | s****h@e****b | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 115
- Total pull requests: 5
- Average time to close issues: 4 months
- Average time to close pull requests: over 2 years
- Total issue authors: 98
- Total pull request authors: 5
- Average comments per issue: 1.51
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 0
- Average time to close issues: 29 days
- Average time to close pull requests: N/A
- Issue authors: 6
- Pull request authors: 0
- Average comments per issue: 0.67
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- renozao (6)
- jacobdornEcon (3)
- kviljoen (3)
- WuyangFF95 (2)
- Gandalfy (2)
- sagar-m (2)
- mkarikom (2)
- kiranvpaul (2)
- ColeWunderlich (2)
- BenxiaHu (2)
- sdoerstling (2)
- capsampension (1)
- AmyOlex (1)
- grimwoo (1)
- zhangshouwei309194 (1)
Pull Request Authors
- nathancday (2)
- russHyde (1)
- khughitt (1)
- ccpalu (1)
- richardbeare (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- cran 8,725 last-month
- Total docker downloads: 161,748
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Total dependent packages: 25
(may contain duplicates) -
Total dependent repositories: 105
(may contain duplicates) - Total versions: 35
- Total maintainers: 1
cran.r-project.org: NMF
Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
- Homepage: http://renozao.github.io/NMF/
- Documentation: http://cran.r-project.org/web/packages/NMF/NMF.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
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Latest release: 0.24.0
published over 4 years ago
Rankings
Maintainers (1)
conda-forge.org: r-nmf
- Homepage: http://renozao.github.io/NMF
- License: GPL-2.0-or-later
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Latest release: 0.21.0
published almost 4 years ago
Rankings
Dependencies
- R >= 3.1.0 depends
- cluster * depends
- methods * depends
- pkgmaker >= 0.31 depends
- registry * depends
- rngtools >= 1.2.3 depends
- utils * depends
- RColorBrewer * imports
- colorspace * imports
- dendextend * imports
- digest * imports
- doParallel >= 1.0.8 imports
- foreach * imports
- ggplot2 * imports
- grDevices * imports
- graphics * imports
- grid * imports
- gridBase * imports
- magrittr * imports
- matrixStats * imports
- reshape2 * imports
- stats * imports
- stringr * imports
- viridis * imports
- Biobase * suggests
- RUnit * suggests
- bibtex * suggests
- bigmemory >= 4.2 suggests
- corpcor * suggests
- devtools * suggests
- fastICA * suggests
- knitr * suggests
- mail * suggests
- synchronicity * suggests
- testthat * suggests
- xtable * suggests