DOI: 10.18129/B9.bioc.simplifyEnrichment  

This is the development version of simplifyEnrichment; for the stable release version, see simplifyEnrichment.

Simplify Functional Enrichment Results

Bioconductor version: Development (3.19)

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.

Author: Zuguang Gu [aut, cre]

Maintainer: Zuguang Gu < at>

Citation (from within R, enter citation("simplifyEnrichment")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script A Shiny app to interactively visualize clustering results
HTML R Script Simplify Functional Enrichment Results
HTML R Script Word Cloud Annotation
PDF   Reference Manual
Text   NEWS


biocViews Clustering, GO, GeneSetEnrichment, Software, Visualization
Version 1.13.1
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License MIT + file LICENSE
Depends R (>= 3.6.0), BiocGenerics, grid
Imports GOSemSim, ComplexHeatmap(>= 2.7.4), circlize, GetoptLong, digest, tm, GO.db,, AnnotationDbi, slam, methods, clue, grDevices, graphics, stats, utils, proxyC, Matrix, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0)
Suggests knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager, InteractiveComplexHeatmap(>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc
Depends On Me
Imports Me
Suggests Me cola, InteractiveComplexHeatmap, pareg
Links To Me
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