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

Simplify Functional Enrichment Results

Bioconductor version: Development (3.20)

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:

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


biocViews Clustering, GO, GeneSetEnrichment, Software, Visualization
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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)
System Requirements
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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
Linking To
Depends On Me
Imports Me
Suggests Me cola, InteractiveComplexHeatmap, pareg, simona, scITD
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package simplifyEnrichment_1.15.0.tar.gz
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macOS Binary (x86_64) simplifyEnrichment_1.15.0.tgz
macOS Binary (arm64) simplifyEnrichment_1.15.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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