BioNERO
Easy and comprehensive biological network reconstruction and analysis
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 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (19.1%) to scientific vocabulary
Keywords from Contributors
bioconductor-package
gene
ontology
immune-repertoire
grna-sequence
evolutionary-genomics
comparative-genomics
differential-proportion
biology
intercellular
Last synced: 11 months ago
·
JSON representation
Repository
Easy and comprehensive biological network reconstruction and analysis
Basic Info
- Host: GitHub
- Owner: almeidasilvaf
- Language: R
- Default Branch: devel
- Homepage: https://almeidasilvaf.github.io/BioNERO/
- Size: 30.1 MB
Statistics
- Stars: 31
- Watchers: 2
- Forks: 5
- Open Issues: 2
- Releases: 0
Created about 6 years ago
· Last pushed almost 2 years ago
Metadata Files
Readme
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#"
)
```
# BioNERO 
[](https://github.com/almeidasilvaf/BioNERO/issues)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://github.com/almeidasilvaf/BioNERO/actions)
[](https://codecov.io/gh/almeidasilvaf/BioNERO?branch=devel)
`BioNERO` aims to integrate all aspects of biological network inference
in a single package, so users don't have to learn the syntaxes of several
packages and how to communicate among them. `BioNERO` features:
- **Expression data preprocessing** using state-of-the-art techniques for
network inference.
- **Automated exploratory data analyses**, including principal component
analysis (PCA) and heatmaps of gene expression or sample correlations.
- **Inference of gene coexpression networks (GCNs)** using the popular WGCNA
algorithm.
- **Inference of gene regulatory networks (GRNs)** based on the "wisdom
of the crowds" principle. This principle consists in inferring GRNs with
multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating
the average rank for each interaction pair.
- **Exploration of network topology** of GCNs, GRNs, and protein-protein
interaction networks.
- **Network visualization**.
- **Network comparison**, including identification of consensus modules
across independent expression sets, and calculation of intra and interspecies
module preservation statistics between different networks.
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `BioNERO` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("BioNERO")
```
And the development version from [GitHub](https://github.com/almeidasilvaf/BioNERO) with:
```{r 'install_dev', eval = FALSE}
BiocManager::install("almeidasilvaf/BioNERO")
```
## Citation
Below is the citation output from using `citation('BioNERO')` in R. Please
run this yourself to check for any updates on how to cite __BioNERO__.
```{r 'citation', eval = requireNamespace('BioNERO')}
print(citation('BioNERO'), bibtex = TRUE)
```
Please note that the `BioNERO` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
Owner
- Name: Fabrício Almeida-Silva
- Login: almeidasilvaf
- Kind: user
- Location: Technologiepark 71, Ghent, Belgium
- Company: VIB-UGent Center for Plant Systems Biology
- Website: https://almeidasilvaf.github.io
- Twitter: almeidasilvaf
- Repositories: 7
- Profile: https://github.com/almeidasilvaf
Bioinformatics. Network biology. Plant genomics and evolution. #rstats addict.
GitHub Events
Total
- Issues event: 9
- Watch event: 4
- Issue comment event: 13
Last Year
- Issues event: 9
- Watch event: 4
- Issue comment event: 13
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| almeidasilvaf | f****a@h****m | 131 |
| Nitesh Turaga | n****a@g****m | 6 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y | 2 |
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 32
- Total pull requests: 1
- Average time to close issues: 13 days
- Average time to close pull requests: 9 days
- Total issue authors: 24
- Total pull request authors: 1
- Average comments per issue: 2.72
- Average comments per pull request: 1.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 7
- Pull requests: 0
- Average time to close issues: 15 days
- Average time to close pull requests: N/A
- Issue authors: 6
- Pull request authors: 0
- Average comments per issue: 1.57
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- 409199 (4)
- Tang-pro (3)
- daniaodeh (2)
- PFRoux (2)
- jucapitanio (2)
- bsangiorgi (1)
- yang050036 (1)
- MysoreSparrow (1)
- Jigyasa3 (1)
- wenjiezeng-cumc (1)
- HelloYiHan (1)
- Galaxy-228 (1)
- WWz33 (1)
- wjq1981 (1)
- LMee17 (1)
Pull Request Authors
- jucapitanio (1)
Top Labels
Issue Labels
question (3)
enhancement (1)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 20,055 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: BioNERO
Biological Network Reconstruction Omnibus
- Homepage: https://github.com/almeidasilvaf/BioNERO
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/BioNERO/inst/doc/BioNERO.pdf
- License: GPL-3
-
Latest release: 1.16.0
published over 1 year ago
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 10.0%
Stargazers count: 12.6%
Average: 19.7%
Downloads: 76.1%
Maintainers (1)
Last synced:
about 1 year ago