https://github.com/bioconductor-source/simplifyenrichment
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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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: other
- Language: R
- Default Branch: devel
- Size: 122 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
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")
Vignette
- Simplify Functional Enrichment Results
- Word Cloud Annotation
- A Shiny app to interactively visualize clustering results
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)
Examples
- Examples of simplifyEnrichment
- Compare different similarity measures for functional terms
- Compare different partitioning methods in binary cut clustering
License
MIT @ Zuguang Gu
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
GitHub Events
Total
Last Year
Dependencies
- 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
- 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
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- ggplot2 * suggests
- gridExtra * suggests
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- hu6800.db * suggests
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- msigdbr * suggests
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