simplifyEnrichment
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see simplifyEnrichment.
Simplify Functional Enrichment Results
Bioconductor version: 3.16
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("simplifyEnrichment")):
Installation
To install this package, start R (version "4.2") 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")| 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GO, GeneSetEnrichment, Software, Visualization |
| Version | 1.8.0 |
| 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 |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | simplifyEnrichment_1.8.0.tar.gz |
| Windows Binary | simplifyEnrichment_1.8.0.zip |
| macOS Binary (x86_64) | simplifyEnrichment_1.8.0.tgz |
| macOS Binary (arm64) | simplifyEnrichment_1.8.0.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 3.16 | Source Archive |