simplifyEnrichment

DOI: 10.18129/B9.bioc.simplifyEnrichment    

Simplify Functional Enrichment Results

Bioconductor version: Release (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>

Citation (from within R, enter citation("simplifyEnrichment")):

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) (< 6 months)
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 (32- & 64-bit)
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

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