FlowSOM

DOI: 10.18129/B9.bioc.FlowSOM    

Using self-organizing maps for visualization and interpretation of cytometry data

Bioconductor version: Release (3.13)

FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.

Author: Sofie Van Gassen [aut, cre], Artuur Couckuyt [aut], Katrien Quintelier [aut], Annelies Emmaneel [aut], Britt Callebaut [aut], Yvan Saeys [aut]

Maintainer: Sofie Van Gassen <sofie.vangassen at ugent.be>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FlowSOM")

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("FlowSOM")

 

PDF	R Script	FlowSOM
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, CellBiology, Clustering, FlowCytometry, Software, Visualization
Version	2.0.0
In Bioconductor since	BioC 3.1 (R-3.2) (6.5 years)
License	GPL (>= 2)
Depends	R (>= 4.0), igraph
Imports	stats, utils, BiocGenerics, colorRamps, ConsensusClusterPlus, CytoML, dplyr, flowCore, flowWorkspace, ggforce, ggnewscale, ggplot2, ggpointdensity, ggpubr, ggrepel, grDevices, magrittr, methods, pheatmap, RColorBrewer, rlang, Rtsne, tidyr, XML, scattermore
LinkingTo
Suggests	BiocStyle, testthat
SystemRequirements
Enhances
URL	http://www.r-project.org http://dambi.ugent.be
Depends On Me
Imports Me	CATALYST, cytofast, CytoTree, diffcyt, MetaCyto
Suggests Me	HDCytoData
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	FlowSOM_2.0.0.tar.gz
Windows Binary	FlowSOM_2.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	FlowSOM_2.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FlowSOM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FlowSOM
Package Short Url	https://bioconductor.org/packages/FlowSOM/
Package Downloads Report	Download Stats