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simplifyEnrichment
This is thereleased version of simplifyEnrichment; for the devel version, seesimplifyEnrichment.
Simplify Functional Enrichment Results
Bioconductor version: Release (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("simplifyEnrichment")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("simplifyEnrichment")For older versions of R, please refer to the appropriateBioconductor 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 | 2.4.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| License | MIT + fileLICENSE |
| 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/simplifyEnrichmenthttps://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
FollowInstallation instructions to use this package in your R session.
| Source Package | simplifyEnrichment_2.4.0.tar.gz |
| Windows Binary (x86_64) | simplifyEnrichment_2.4.0.zip |
| macOS Binary (x86_64) | simplifyEnrichment_2.4.0.tgz |
| macOS Binary (arm64) | simplifyEnrichment_2.4.0.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 |