simplifyEnrichment
Simplify Functional Enrichment Results
Bioconductor version: Release (3.19)
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.
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")
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 | 1.14.1 |
In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.14.1.tar.gz |
Windows Binary | simplifyEnrichment_1.14.1.zip |
macOS Binary (x86_64) | simplifyEnrichment_1.14.1.tgz |
macOS Binary (arm64) | simplifyEnrichment_1.14.1.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 3.19 | Source Archive |