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enrichViewNet

From functional enrichment results to biological networks

https://github.com/adeschen/enrichviewnet

Science Score: 26.0%

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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    Found codemeta.json file
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    Found .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (9.9%) to scientific vocabulary

Keywords

cystocape functional-enrichment network r-package
Last synced: 6 months ago · JSON representation

Repository

From functional enrichment results to biological networks

Basic Info
Statistics
  • Stars: 5
  • Watchers: 3
  • Forks: 1
  • Open Issues: 3
  • Releases: 7
Topics
cystocape functional-enrichment network r-package
Created almost 5 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog

README.md

R-CMD-check-bioc codecov License: Artistic-2.0 <!-- badges: end -->

The enrichViewNet package enables the transformation of functional enrichment results, formatted as the results obtained by gprofiler2, into networks.

First, the enrichViewNet package enables the visualization of enrichment results a Cytoscape 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 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

Bioconductor Time

The enrichViewNet package is now an official package of Bioconductor.

The current Bioconductor release can be directly downloaded from their website: Current release

Authors

Astrid Deschênes, Pascal Belleau, Robert L Faure, Maria J Fernandes, Alexander Krasnitz and David A Tuveson

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

Documentation

enrichViewNet Website

enrichViewNet Get Started

Installation

To install the latest version accessible, the devtools 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, 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.

Thanks!

Owner

  • Name: Astrid Deschênes
  • Login: adeschen
  • Kind: user
  • Location: New York
  • Company: Cold Spring Harbor Laboratory

I am a Computational Science Analyst at Cold Spring Harbor Laboratory.

GitHub Events

Total
  • Push event: 14
Last Year
  • Push event: 14

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 6
  • Total pull requests: 14
  • Average time to close issues: 11 months
  • Average time to close pull requests: about 2 hours
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.36
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 20 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • adeschen (5)
  • yungsiyebu (1)
Pull Request Authors
  • adeschen (9)
  • belleau (6)
Top Labels
Issue Labels
Pull Request Labels
enhancement (2)

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 4,359 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
bioconductor.org: enrichViewNet

From functional enrichment results to biological networks

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4,359 Total
Rankings
Dependent repos count: 0.0%
Average: 21.7%
Stargazers count: 25.2%
Forks count: 30.1%
Dependent packages count: 31.7%
Maintainers (1)
adeschen@hotmail.com
Last synced: 7 months ago

Dependencies

.github/workflows/check-bioc.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 4.0 depends
  • RCy3 * imports
  • gprofiler2 * imports
  • jsonlite * imports
  • methods * imports
  • strex * imports
  • stringr * imports
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests