FlowSOM

DOI: 10.18129/B9.bioc.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 (3.14)

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 "4.1") and enter:

if (!requireNamespace("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")

 

PDF R Script FlowSOM
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBasedAssays, CellBiology, Clustering, FlowCytometry, Software, Visualization
Version 2.1.24
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, 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_2.1.24.tar.gz
Windows Binary FlowSOM_2.1.24.zip (32- & 64-bit)
macOS 10.13 (High Sierra) FlowSOM_2.1.24.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

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