https://github.com/adeschen/enrichviewnet
From functional enrichment results to biological networks
https://github.com/adeschen/enrichviewnet
cystocape functional-enrichment network r-package
Last synced: 2 months ago
JSON representation
From functional enrichment results to biological networks
- Host: GitHub
- URL: https://github.com/adeschen/enrichviewnet
- Owner: adeschen
- Created: 2021-03-26T20:08:22.000Z (about 4 years ago)
- Default Branch: devel
- Last Pushed: 2024-04-11T02:01:55.000Z (about 1 year ago)
- Last Synced: 2024-04-12T07:23:11.203Z (about 1 year ago)
- Topics: cystocape, functional-enrichment, network, r-package
- Language: R
- Homepage: https://adeschen.github.io/enrichViewNet/
- Size: 14.9 MB
- Stars: 5
- Watchers: 3
- Forks: 1
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
[](https://github.com/adeschen/enrichViewNet/actions/workflows/check-bioc.yml)
[](https://codecov.io/gh/adeschen/enrichViewNet)
[](https://opensource.org/licenses/Artistic-2.0)
The **enrichViewNet** package enables the transformation of
functional enrichment results, formatted as the results obtained by [gprofiler2](https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html),
into networks.
First, the **enrichViewNet** package enables the
visualization of enrichment results a [Cytoscape](https://cytoscape.org/)
network where significant terms
(Gene Ontology/Reactome/Transcription Factor/etc..) and
genes are nodes. In this network, edges connect genes that are part of the
enrichment request to their terms.
In addition, the **enrichViewNet** package also provides the option to
create enrichment maps from functional enrichment results.
Enrichment maps, as introduced in the Bioconductor
[enrichplot](https://bioconductor.org/packages/release/bioc/html/enrichplot.html) package,
enable the visualization of enriched terms
into a network with edges connecting overlapping genes. Thus, enriched terms
with overlapping genes cluster together.
## Bioconductor Package ##
[](https://bioconductor.org/packages/enrichViewNet)
The **enrichViewNet** package is now an official package
of [Bioconductor](http://bioconductor.org/).
The current Bioconductor release can be directly downloaded from their website:
[Current release](https://bioconductor.org/packages/enrichViewNet/)
## Authors ##
[Astrid Deschênes](http://ca.linkedin.com/in/astriddeschenes "Astrid Deschênes"),
[Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau "Pascal Belleau"),
[Robert L Faure](https://www.crchudequebec.ulaval.ca/en/research/researchers/robert-l-faure/),
[Maria J Fernandes](https://www.crchudequebec.ulaval.ca/en/research/researchers/maria-fernandes/),
[Alexander Krasnitz](https://www.cshl.edu/research/faculty-staff/alexander-krasnitz/) and
[David A Tuveson](https://tuvesonlab.labsites.cshl.edu/)
## License ##
This package and the underlying **enrichViewNet** code are distributed under
the Artistic license 2.0. You are free to use and redistribute this software.
For more information on Artistic 2.0 License see
[http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0)
## Documentation ##
[enrichViewNet Website](https://adeschen.github.io/enrichViewNet/)
[enrichViewNet Get Started](https://adeschen.github.io/enrichViewNet/articles/enrichViewNet.html)
## Installation ##
To install the latest version accessible, the
[devtools](https://cran.r-project.org/web/packages/devtools/index.html)
package is required.
## Load required package
library(devtools)
## Install the latest version of enrichViewNet
devtools::install_github('adeschen/enrichViewNet')
To install this package
from [Bioconductor](https://bioconductor.org), start R
(version 4.3 or later) and enter:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("enrichViewNet")
## Bugs/Feature requests ##
If you have any bugs or feature requests,
[let us know](https://github.com/adeschen/enrichViewNet/issues).
Thanks!