simplifyEnrichment
This is the released version of simplifyEnrichment; for the devel version, see simplifyEnrichment.
Simplify Functional Enrichment Results
Bioconductor version: Release (3.23)
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 <guzuguang at suat-sz.edu.cn>
citation("simplifyEnrichment")):Zuguang Gu. simplifyEnrichment: Simplify Functional Enrichment Results. doi:10.18129/B9.bioc.simplifyEnrichment, R package version 2.6.0, https://bioconductor.org/packages/simplifyEnrichment.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | Clustering, GO, GeneSetEnrichment, Software, Visualization |
| Version | 2.6.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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 |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | simplifyEnrichment_2.6.0.tar.gz |
| Windows Binary (x86_64) | simplifyEnrichment_2.6.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | simplifyEnrichment_2.6.0.tgz |
| macOS Binary (sonoma-arm64) | simplifyEnrichment_2.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/simplifyEnrichment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/simplifyEnrichment |
| Package Short Url | https://bioconductor.org/packages/simplifyEnrichment/ |
| Package Downloads Report | Download Stats |