simplifyEnrichment
Simplify functional enrichment results
Science Score: 39.0%
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
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.6%) to scientific vocabulary
Keywords from Contributors
Repository
Simplify functional enrichment results
Basic Info
- Host: GitHub
- Owner: jokergoo
- License: other
- Language: R
- Default Branch: master
- Homepage: https://jokergoo.github.io/simplifyEnrichment
- Size: 133 MB
Statistics
- Stars: 117
- Watchers: 3
- Forks: 17
- Open Issues: 51
- Releases: 1
Metadata Files
README.md
Simplify Functional Enrichment Results
Features
- A new method (binary cut) is proposed to efficiently cluster functional terms (e.g. GO terms) into groups from the semantic similarity matrix.
- Summaries of functional terms in each cluster are visualized by word clouds.
Citation
Zuguang Gu, et al., simplifyEnrichment: an R/Bioconductor package for Clustering and Visualizing Functional Enrichment Results, Genomics, Proteomics & Bioinformatics 2022. https://doi.org/10.1016/j.gpb.2022.04.008.
Install
simplifyEnrichment is available on Bioconductor, you can install it by:
r
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("simplifyEnrichment")
If you want to try the latest version, install it directly from GitHub:
r
library(devtools)
install_github("jokergoo/simplifyEnrichment")
Usage
As an example, I first generate a list of random GO IDs.
```r library(simplifyEnrichment) set.seed(888) goid = randomGO(500) head(go_id)
[1] "GO:0003283" "GO:0060032" "GO:0031334" "GO:0097476" "GO:1901222"
[6] "GO:0018216"
```
Then generate the GO similarity matrix, split GO terms into clusters and visualize it.
r
mat = GO_similarity(go_id)
simplifyGO(mat)
License
MIT @ Zuguang Gu
Owner
- Name: Zuguang Gu
- Login: jokergoo
- Kind: user
- Location: Heidelberg, Germany
- Company: German Cancer Research Center
- Website: http://jokergoo.github.io
- Repositories: 28
- Profile: https://github.com/jokergoo
A bioinformagician
GitHub Events
Total
- Issues event: 3
- Watch event: 7
- Issue comment event: 4
- Fork event: 1
Last Year
- Issues event: 3
- Watch event: 7
- Issue comment event: 4
- Fork event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Zuguang Gu | j****o@g****m | 213 |
| Nitesh Turaga | n****a@g****m | 8 |
| J Wokaty | j****y | 8 |
| krassowski | k****l@g****m | 2 |
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 106
- Total pull requests: 3
- Average time to close issues: about 2 months
- Average time to close pull requests: 3 months
- Total issue authors: 50
- Total pull request authors: 3
- Average comments per issue: 0.79
- Average comments per pull request: 2.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 8
- Pull requests: 1
- Average time to close issues: 17 days
- Average time to close pull requests: N/A
- Issue authors: 7
- Pull request authors: 1
- Average comments per issue: 0.88
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jokergoo (44)
- krassowski (9)
- GuiSeSanz (3)
- GreenGilad (2)
- j-andrews7 (2)
- BBJamge (1)
- aa20g217 (1)
- yesitsjess (1)
- jelman (1)
- tfguinan (1)
- xcliu-oc (1)
- drkgil (1)
- sugiYag (1)
- Knight1995 (1)
- yaaminiv (1)
Pull Request Authors
- krassowski (1)
- tfguinan (1)
- GreenGilad (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 51,564 total
- Total dependent packages: 4
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: simplifyEnrichment
Simplify Functional Enrichment Results
- Homepage: https://github.com/jokergoo/simplifyEnrichment https://simplifyEnrichment.github.io
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/simplifyEnrichment/inst/doc/simplifyEnrichment.pdf
- License: MIT + file LICENSE
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Latest release: 2.2.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- BiocGenerics * depends
- R >= 3.6.0 depends
- grid * depends
- AnnotationDbi * imports
- ComplexHeatmap >= 2.7.4 imports
- GO.db * imports
- GOSemSim * imports
- GetoptLong * imports
- GlobalOptions >= 0.1.0 imports
- Matrix * imports
- circlize * imports
- clue * imports
- cluster >= 1.14.2 imports
- colorspace * imports
- digest * imports
- grDevices * imports
- graphics * imports
- methods * imports
- org.Hs.eg.db * imports
- proxyC * imports
- slam * imports
- stats * imports
- tm * imports
- utils * imports
- BiocManager * suggests
- DO.db * suggests
- DOSE * suggests
- InteractiveComplexHeatmap >= 0.99.11 suggests
- MCL * suggests
- apcluster * suggests
- clusterProfiler * suggests
- cola * suggests
- cowplot * suggests
- dbscan * suggests
- dynamicTreeCut * suggests
- flexclust * suggests
- fpc * suggests
- genefilter * suggests
- ggplot2 * suggests
- gridExtra * suggests
- gridGraphics * suggests
- gridtext * suggests
- hu6800.db * suggests
- igraph * suggests
- knitr * suggests
- mclust * suggests
- msigdbr * suggests
- reactome.db * suggests
- rmarkdown * suggests
- shiny * suggests
- shinydashboard * suggests
- testthat * suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact main composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite