simplifyEnrichment

Simplify Functional Enrichment Results

Bioconductor version: 3.23 · Package version: 2.6.0

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
Downloads rank	1454
Source branch	RELEASE_3_23
biocViews	Clustering, GO, GeneSetEnrichment, Software, Visualization

Documentation

The simplifyEnrichment package

Download

Source package

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 (4): cola, InteractiveComplexHeatmap, scITD, simona