FlowSOM

This is the released version of FlowSOM; for the devel version, see FlowSOM.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

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

Bioconductor version: Release (3.23)

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], Sarah Bonte [aut], Robbe Fonteyn [aut], Britt Callebaut [aut], Yvan Saeys [aut]

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

Citation (from within R, enter citation("FlowSOM")):

Sofie Van Gassen, Artuur Couckuyt, Katrien Quintelier, Annelies Emmaneel, Sarah Bonte, Robbe Fonteyn, Britt Callebaut, Yvan Saeys. FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data. doi:10.18129/B9.bioc.FlowSOM, R package version 2.20.0, https://bioconductor.org/packages/FlowSOM.

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("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")

FlowSOM	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, CellBiology, Clustering, FlowCytometry, Software, Visualization
Version	2.20.0
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 years)
License	GPL (>= 2)
Depends	R (>= 4.5), igraph
Imports	stats, utils, colorRamps, ConsensusClusterPlus, dplyr, flowCore, ggforce, ggnewscale, ggplot2, ggpubr, grDevices, magrittr, methods, rlang, Rtsne, tidyr, BiocGenerics, XML
System Requirements
URL	http://www.r-project.org http://dambi.ugent.be

Suggests	BiocStyle, testthat, CytoML, flowWorkspace, ggrepel, scattermore, pheatmap, ggpointdensity, ComplexHeatmap
Linking To
Enhances
Depends On Me
Imports Me	CATALYST, diffcyt, MetaCyto
Suggests Me	HDCytoData, tidytof
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	FlowSOM_2.20.0.tar.gz
Windows Binary (x86_64)	FlowSOM_2.20.0.zip
macOS Binary (big-sur-x86_64)	FlowSOM_2.20.0.tgz
macOS Binary (sonoma-arm64)	FlowSOM_2.20.0.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