Registration Open for Bioc2024
Early registration discount pricing ends May 31!

simplifyEnrichment

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

Simplify Functional Enrichment Results


Bioconductor version: Development (3.20)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")
A Shiny app to interactively visualize clustering results HTML R Script
Simplify Functional Enrichment Results HTML R Script
Word Cloud Annotation HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, GO, GeneSetEnrichment, Software, Visualization
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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)
System Requirements
URL https://github.com/jokergoo/simplifyEnrichment https://simplifyEnrichment.github.io
See More
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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me cola, InteractiveComplexHeatmap, pareg, simona, scITD
Links To Me
Build Report Build Report

Package Archives

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

Source Package simplifyEnrichment_1.15.0.tar.gz
Windows Binary simplifyEnrichment_1.15.0.zip
macOS Binary (x86_64) simplifyEnrichment_1.15.0.tgz
macOS Binary (arm64) simplifyEnrichment_1.15.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/simplifyEnrichment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/simplifyEnrichment
Bioc Package Browser https://code.bioconductor.org/browse/simplifyEnrichment/
Package Short Url https://bioconductor.org/packages/simplifyEnrichment/
Package Downloads Report Download Stats