simplifyEnrichment

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see simplifyEnrichment.

Simplify Functional Enrichment Results


Bioconductor version: 3.13

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 "4.1") 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")
1. Simplify Functional Enrichment Results HTML R Script
2. Word Cloud Annotation HTML R Script
3. A Shiny app to interactively visualize clustering results HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, GO, GeneSetEnrichment, Software, Visualization
Version 1.2.0
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)
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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me cola, InteractiveComplexHeatmap
Links To Me
Build Report Build Report

Package Archives

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

Source Package simplifyEnrichment_1.2.0.tar.gz
Windows Binary simplifyEnrichment_1.2.0.zip
macOS 10.13 (High Sierra) simplifyEnrichment_1.2.0.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
Old Source Packages for BioC 3.13 Source Archive