simplifyEnrichment

This is the released version of simplifyEnrichment; for the devel version, see simplifyEnrichment.

Simplify Functional Enrichment Results

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DOI: 10.18129/B9.bioc.simplifyEnrichment

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-7395-8709

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

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

Installation

To install this package, start R (version "4.5") 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")

The simplifyEnrichment package HTML

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, GO, GeneSetEnrichment, Software, Visualization

Version 2.4.0

In Bioconductor since BioC 3.12 (R-4.0) (5 years)

License MIT + file LICENSE

Depends R (>= 4.1.0)

Imports simona, ComplexHeatmap(>= 2.7.4), grid, circlize, GetoptLong, digest, tm, GO.db, AnnotationDbi, slam, methods, clue, grDevices, stats, utils, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0)

System Requirements

URL https://github.com/jokergoo/simplifyEnrichment https://simplifyEnrichment.github.io

Suggests knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, 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, simona, scITD

Links To Me

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Package Archives

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

Source Package simplifyEnrichment_2.4.0.tar.gz

Windows Binary (x86_64) simplifyEnrichment_2.4.0.zip (64-bit only)

macOS Binary (x86_64) simplifyEnrichment_2.4.0.tgz

macOS Binary (arm64) simplifyEnrichment_2.4.0.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/

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