DOI: 10.18129/B9.bioc.simplifyEnrichment  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see simplifyEnrichment.

Simplify Functional Enrichment Results

Bioconductor version: 3.16

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")):


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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 1.8.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 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)
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
Links To Me
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