simplifyEnrichment
Simplify Functional Enrichment Results
Bioconductor version: 3.23 · Package version: 2.6.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("simplifyEnrichment")Details
| Maintainer | Zuguang Gu <guzuguang@suat-sz.edu.cn> |
| Author | Zuguang Gu [aut, cre] (ORCID: <https://orcid.org/0000-0002-7395-8709>) |
| License | MIT + file LICENSE |
| URL | https://github.com/jokergoo/simplifyEnrichment, https://simplifyEnrichment.github.io |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, GO, GeneSetEnrichment, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/simplifyEnrichment/ |
Citation
From within R, enter citation("simplifyEnrichment"):
Zuguang Gu. simplifyEnrichment: Simplify Functional Enrichment Results. doi:10.18129/B9.bioc.simplifyEnrichment, R package version 2.6.0, https://bioconductor.org/packages/simplifyEnrichment.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | simplifyEnrichment_2.6.0.tar.gz |
| Windows binary (x86_64) | simplifyEnrichment_2.6.0.zip |
| macOS binary (arm64) | simplifyEnrichment_2.6.0.tgz |
| macOS binary (x86_64) | simplifyEnrichment_2.6.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong, digest, tm, GO.db, AnnotationDbi, slam, methods, clue, grDevices, stats, utils, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0)
Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc
Reverse dependencies
Suggests Me (3): cola, InteractiveComplexHeatmap, simona