simplifyEnrichment

DOI: 10.18129/B9.bioc.simplifyEnrichment    

This is the development version of simplifyEnrichment; for the stable release version, see simplifyEnrichment.

Simplify Functional Enrichment Results

Bioconductor version: Development (3.15)

A new clustering algorithm, binary cut, for clustering similarity matrices of functional terms is implemeted in this package. It also provideds functionalities for visualizing, summarizing and comparing the clusterings.

Author: Zuguang Gu [aut, cre]

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

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1. Simplify Functional Enrichment Results
HTML R Script 2. Word Cloud Annotation
HTML R Script 3. A Shiny app to interactively visualize clustering results
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Clustering, GO, GeneSetEnrichment, Software, Visualization
Version 1.5.0
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
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)
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
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_1.5.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) simplifyEnrichment_1.5.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: