Science Score: 49.0%
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
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 6 committers (16.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.9%) to scientific vocabulary
Keywords from Contributors
Repository
Reduce + Visualize Gene Ontology
Basic Info
- Host: GitHub
- Owner: ssayols
- License: gpl-3.0
- Language: R
- Default Branch: master
- Size: 19 MB
Statistics
- Stars: 31
- Watchers: 2
- Forks: 4
- Open Issues: 2
- Releases: 1
Metadata Files
README.md
RRVGO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Introduction to rrvgo
Gene Ontologies (GO) are often used to guide the interpretation of high-throughput omics experiments, with lists of differentially regulated genes being summarized into sets of genes with a common functional representation. Due to the hierachical nature of Gene Ontologies, the resulting lists of enriched sets are usually redundant and difficult to interpret.
rrvgo aims at simplifying the redundance of GO sets by grouping similar terms
in terms of semantic similarity. It also provides some plots to help with
interpreting the summarized terms.
This software is heavily influenced by REVIGO. It mimics
a good part of its core functionality, and even some of the outputs are similar.
Without aims to compete, rrvgo tries to offer a programatic interface using
available annotation databases and semantic similarity methods implemented in the
Bioconductor project.
Installation
To install this package, start R and enter:
```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("rrvgo") ```
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
r
browseVignettes("rrvgo")
or access the pkgdown documentation.
Dependencies
Imports (mandatory for core functionality)
- GOSemSim: Semantic similarity computation among GO terms.
- AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
- GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.
Suggests
- pheatmap
- wordcloud
- treemap
- ggplot2
- shiny
- heatmaply
- plotly
- org.Ag.eg.db: Genome wide annotation for Anopheles.
- org.At.tair.db: Genome wide annotation for Arabidopsis.
- org.Bt.eg.db: Genome wide annotation for Bovine.
- org.Ce.eg.db: Genome wide annotation for Worm.
- org.Cf.eg.db: Genome wide annotation for Canine.
- org.Dm.eg.db: Genome wide annotation for Fly.
- org.Dr.eg.db: Genome wide annotation for Zebrafish.
- org.EcK12.eg.db: Genome wide annotation for E coli strain K12.
- org.EcSakai.eg.db: Genome wide annotation for E coli strain Sakai.
- org.Gg.eg.db: Genome wide annotation for Chicken.
- org.Hs.eg.db: Genome wide annotation for Human.
- org.Mm.eg.db: Genome wide annotation for Mouse.
- org.Mmu.eg.db: Genome wide annotation for Rhesus.
- org.Pf.plasmo.db: Genome wide annotation for Malaria.
- org.Pt.eg.db: Genome wide annotation for Chimp.
- org.Rn.eg.db: Genome wide annotation for Rat.
- org.Sc.sgd.db: Genome wide annotation for Yeast.
- org.Ss.eg.db: Genome wide annotation for Pig.
- org.Xl.eg.db: Genome wide annotation for Xenopus.
Citation
Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.
Owner
- Name: ssayols
- Login: ssayols
- Kind: user
- Repositories: 33
- Profile: https://github.com/ssayols
GitHub Events
Total
- Create event: 2
- Issues event: 4
- Release event: 1
- Watch event: 9
- Issue comment event: 6
- Push event: 32
- Fork event: 1
Last Year
- Create event: 2
- Issues event: 4
- Release event: 1
- Watch event: 9
- Issue comment event: 6
- Push event: 32
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 44
- Total pull requests: 8
- Average time to close issues: about 1 month
- Average time to close pull requests: about 3 hours
- Total issue authors: 24
- Total pull request authors: 3
- Average comments per issue: 2.59
- Average comments per pull request: 0.25
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 0
- Average time to close issues: about 6 hours
- Average time to close pull requests: N/A
- Issue authors: 5
- Pull request authors: 0
- Average comments per issue: 1.2
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kkami1115 (2)
- gaelanm (2)
- eliotbehr (1)
- sophie-03 (1)
- Tommaso12 (1)
- aedanr (1)
- Tima-Ze (1)
- rdona17 (1)
- Maithy15 (1)
- aa20g217 (1)
- RoganGrant (1)
- tamsinlh (1)
- lassancejm (1)
- abrantesas (1)
- KTMD-plant (1)
Pull Request Authors
- EinarBaldvin (2)
- ssayols (2)
- illumination-k (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 31,455 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: rrvgo
Reduce + Visualize GO
- Homepage: https://www.bioconductor.org/packages/rrvgo https://ssayols.github.io/rrvgo/index.html
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/rrvgo/inst/doc/rrvgo.pdf
- License: GPL-3
-
Latest release: 1.20.0
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- AnnotationDbi * imports
- GO.db * imports
- GOSemSim * imports
- ggplot2 * imports
- ggrepel * imports
- grDevices * imports
- grid * imports
- methods * imports
- pheatmap * imports
- shiny * imports
- stats * imports
- tm * imports
- treemap * imports
- umap * imports
- wordcloud * imports
- BiocStyle * suggests
- DOSE * suggests
- DT * suggests
- clusterProfiler * suggests
- heatmaply * suggests
- knitr * suggests
- magrittr * suggests
- org.Ag.eg.db * suggests
- org.At.tair.db * suggests
- org.Bt.eg.db * suggests
- org.Ce.eg.db * suggests
- org.Cf.eg.db * suggests
- org.Dm.eg.db * suggests
- org.Dr.eg.db * suggests
- org.EcK12.eg.db * suggests
- org.EcSakai.eg.db * suggests
- org.Gg.eg.db * suggests
- org.Hs.eg.db * suggests
- org.Mm.eg.db * suggests
- org.Mmu.eg.db * suggests
- org.Pt.eg.db * suggests
- org.Rn.eg.db * suggests
- org.Sc.sgd.db * suggests
- org.Ss.eg.db * suggests
- org.Xl.eg.db * suggests
- plotly * suggests
- rmarkdown * suggests
- shinydashboard * suggests
- slam * suggests
- testthat >= 2.1.0 suggests
- utils * suggests
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