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Bioconductor - simplifyEnrichment (development version)

simplifyEnrichment

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

Simplify Functional Enrichment Results

Bioconductor version: Development (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: 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")

# 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")
The simplifyEnrichment package HTML Reference Manual PDF NEWS Text LICENSE Text Details biocViews Clustering, GO, GeneSetEnrichment, Software, Visualization Version 2.3.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 See More 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 Build Report Build Report Package Archives

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

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