simplifyEnrichment

DOI: 10.18129/B9.bioc.simplifyEnrichment    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see simplifyEnrichment.

Simplify Functional Enrichment Results

Bioconductor version: 3.12

A new method (binary cut) is proposed to effectively cluster GO terms into groups from the semantic similarity matrix. Summaries of GO terms in each cluster are visualized by word clouds.

Author: Zuguang Gu

Maintainer: Zuguang Gu <z.gu at dkfz.de>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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	Simplify Functional Enrichment Results
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, GO, GeneSetEnrichment, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0), BiocGenerics, grid
Imports	GOSemSim, ComplexHeatmap(>= 2.5.4), circlize, GetoptLong, digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods, clue, grDevices, graphics, stats, utils, proxyC, Matrix, cluster (>= 1.14.2)
LinkingTo
Suggests	knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager
SystemRequirements
Enhances
URL	https://github.com/jokergoo/simplifyEnrichment https://simplifyEnrichment.github.io
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	simplifyEnrichment_1.0.0.tar.gz
Windows Binary	simplifyEnrichment_1.0.0.zip
macOS 10.13 (High Sierra)	simplifyEnrichment_1.0.0.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