simplifyEnrichment
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see simplifyEnrichment.
Simplify Functional Enrichment Results
Bioconductor version: 3.12
A new method (binary cut) is proposed to effectively cluster GO terms into groups from the semantic similarity matrix. Summaries of GO terms in each cluster are visualized by word clouds.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu at dkfz.de>
citation("simplifyEnrichment")):
Installation
To install this package, start R (version "4.0") 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")| Simplify Functional Enrichment Results | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GO, GeneSetEnrichment, Software, Visualization |
| Version | 1.0.0 |
| 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(>= 2.5.4), circlize, GetoptLong, digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods, clue, grDevices, graphics, stats, utils, proxyC, Matrix, cluster (>= 1.14.2) |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | simplifyEnrichment_1.0.0.tar.gz |
| Windows Binary | simplifyEnrichment_1.0.0.zip |
| macOS 10.13 (High Sierra) | simplifyEnrichment_1.0.0.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 3.12 | Source Archive |