simplifyEnrichment
This is the development version of simplifyEnrichment; for the stable release version, see simplifyEnrichment.
Simplify Functional Enrichment Results
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 2.7.0 |
| 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, scITD |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | simplifyEnrichment_2.7.0.tar.gz |
| Windows Binary (x86_64) | simplifyEnrichment_2.7.0.zip |
| macOS Binary (big-sur-x86_64) | simplifyEnrichment_2.7.0.tgz |
| macOS Binary (sonoma-arm64) | simplifyEnrichment_2.7.0.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 |