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FlowSOM

This is the development version of FlowSOM; for the stable release version, see FlowSOM.

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


Bioconductor version: Development (3.20)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews CellBasedAssays, CellBiology, Clustering, FlowCytometry, Software, Visualization
Version 2.13.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL (>= 2)
Depends R (>= 4.0), 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
See More
Suggests BiocStyle, testthat, CytoML, flowWorkspace, ggrepel, scattermore, pheatmap, ggpointdensity
Linking To
Enhances
Depends On Me
Imports Me CATALYST, diffcyt
Suggests Me HDCytoData
Links To Me
Build Report Build Report

Package Archives

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

Source Package FlowSOM_2.13.0.tar.gz
Windows Binary FlowSOM_2.13.0.zip (64-bit only)
macOS Binary (x86_64) FlowSOM_2.13.0.tgz
macOS Binary (arm64) FlowSOM_2.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/FlowSOM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FlowSOM
Bioc Package Browser https://code.bioconductor.org/browse/FlowSOM/
Package Short Url https://bioconductor.org/packages/FlowSOM/
Package Downloads Report Download Stats