simplifyEnrichment

DOI: 10.18129/B9.bioc.simplifyEnrichment    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see simplifyEnrichment.

Simplify Functional Enrichment Results

Bioconductor version: 3.15

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 <z.gu at dkfz.de>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("simplifyEnrichment")

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

Documentation

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

browseVignettes("simplifyEnrichment")

 

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
Text		LICENSE

Details

biocViews	Clustering, GO, GeneSetEnrichment, Software, Visualization
Version	1.6.1
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0), BiocGenerics, grid
Imports	GOSemSim, ComplexHeatmap(>= 2.7.4), circlize, GetoptLong, digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods, clue, grDevices, graphics, stats, utils, proxyC, Matrix, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0)
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/jokergoo/simplifyEnrichment https://simplifyEnrichment.github.io
Depends On Me
Imports Me
Suggests Me	cola, InteractiveComplexHeatmap
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	simplifyEnrichment_1.6.1.tar.gz
Windows Binary	simplifyEnrichment_1.6.1.zip
macOS Binary (x86_64)	simplifyEnrichment_1.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/simplifyEnrichment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/simplifyEnrichment
Package Short Url	https://bioconductor.org/packages/simplifyEnrichment/
Package Downloads Report	Download Stats