Science Score: 18.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
○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
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.8%) to scientific vocabulary
Keywords from Contributors
Repository
BioNetStat
Basic Info
- Host: GitHub
- Owner: jardimViniciusC
- Language: R
- Default Branch: master
- Size: 45 MB
Statistics
- Stars: 8
- Watchers: 1
- Forks: 3
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
BioNetStat
Package to perform network analysis.
BioNetStat is able to compare two or more correlation networks.
The diversity of interactions that occurs in biological systems from the cells and organelles to the whole biosphere, can be assessed with tools of the networks theory. The dynamic in structure and in the interactions among systems elements is an inherent trait of those systems. Several tools have been proposed to compare networks, representing the many states assumed by a system. However, until the present, none of them is able to compare structural characteristics among more than two networks simultaneously. Due to the many states that can be assumed by a given biological system, we developed a statistical tool to compare two or more networks and point key variables in a system. BioNetStat is able to compare correlation networks using traits that are based on graph spectra (the group of eigenvalues in an adjacency matrix), such as the spectral distribution. This measure is associated with several structural characteristics of networks such as the number of walks, diameter, and clicks. In addition to the spectral distribution, BioNetStat can also compare networks by using spectral entropy, degree distribution, and nodes centralities. Until now the BioNetStat theoretical base is available only in the master dissertation, in Portuguese. The paper is under production and will be posted here as soon as possible.
Authors: Jardim, V., Santos, S., Fujita, A., Buckeridge, S. (2018). BioNetStat: A tool for biological network analysis.
Maintainer: Laboratório de fisiologia ecologica de plantas LAFIECO
Installation
Dependencies
R (>= 3.4), shiny, igraph, shinyBS, pathview
Installation steps
- If don't have the R software installed in our computer, download and install it (check out the R home page)
Open the R command line interface, and install all BNS dependencies (if they have not been installed yet):
Rscript if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("BioNetStat")a.'Pathview' package is an important package to 'Bionetstat' visualzations. In Linux OS, if 'pathview' don't install in installation process, try to install this libraries in linux shell terminal.
Rscript $ sudo apt-get install libxml2-dev $ sudo apt-get install libcurl4-openssl-dev $ sudo apt-get install libssl-devb. And, try to install 'pathview' again
Rscript if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("pathview")Running BioNetStat
After installed and the next time you want to use BioNetStat, to run, just type the following code:
Rscript
library(BioNetStat)
library(shiny)
If you want to use a Graphical interface type
Rscript
runBioNetStat()
Wait for the browser page to open, and enjoy BioNetStat!
How to use BioNetStat?
The tutorial with examples data sets are in the vignette.
Owner
- Name: Vinicius Jardim Carvalho
- Login: jardimViniciusC
- Kind: user
- Repositories: 1
- Profile: https://github.com/jardimViniciusC
Citation (CITATION)
citEntry(entry="article",
Title = "BioNetStat: A Tool for Biological Networks Differential Analysis",
Author = personList(as.person("Vinícius Carvalho Jardim"),
as.person("Suzana de Siqueira Santos"),
as.person("André Fujita"),
as.person("Marcos Silveira Buckeridge")),
Year = 2019,
Journal = "Frontiers in Genetics",
Pages = {"594"},
Volume = {"10"},
doi="10.3389/fgene.2019.00594",
url="https://www.frontiersin.org/article/10.3389/fgene.2019.00594",
textVersion = "Jardim, V. C., Santos, S. d. S., Fujita, A., e Buckeridge, M. S. (2019). BioNetStat: A Tool for Biological
Networks Differential Analysis. Frontiers in Genetics, 10(June):594."
)
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Vinicius Jardim Carvalho | v****c@g****m | 435 |
| Nitesh Turaga | n****a@g****m | 14 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| LiNk-NY | m****9@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: almost 2 years ago
All Time
- Total issues: 1
- Total pull requests: 0
- Average time to close issues: 12 months
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Skourtis (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 9,353 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
- Total maintainers: 1
bioconductor.org: BioNetStat
Biological Network Analysis
- Homepage: http://github.com/jardimViniciusC/BioNetStat
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/BioNetStat/inst/doc/BioNetStat.pdf
- License: GPL (>= 3)
- Status: removed
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Latest release: 1.24.0
published about 2 years ago