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FuseSOM

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

A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets


Bioconductor version: Development (3.19)

A correlation-based multiview self-organizing map for the characterization of cell types in highly multiplexed in situ imaging cytometry assays (`FuseSOM`) is a tool for unsupervised clustering. `FuseSOM` is robust and achieves high accuracy by combining a `Self Organizing Map` architecture and a `Multiview` integration of correlation based metrics. This allows FuseSOM to cluster highly multiplexed in situ imaging cytometry assays.

Author: Elijah Willie [aut, cre]

Maintainer: Elijah Willie <ewil3501 at uni.sydney.edu.au>

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

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("FuseSOM")

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("FuseSOM")
FuseSOM package manual HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, Clustering, SingleCell, Software, Spatial
Version 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License GPL-2
Depends R (>= 4.2.0)
Imports psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster, fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest, methods, SummarizedExperiment, stats, S4Vectors
System Requirements
URL
Bug Reports https://github.com/ecool50/FuseSOM/issues
See More
Suggests knitr, BiocStyle, rmarkdown, SingleCellExperiment
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me spicyWorkflow
Links To Me
Build Report Build Report

Package Archives

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

Source Package FuseSOM_1.5.0.tar.gz
Windows Binary FuseSOM_1.5.0.zip
macOS Binary (x86_64) FuseSOM_1.5.0.tgz
macOS Binary (arm64) FuseSOM_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/FuseSOM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FuseSOM
Bioc Package Browser https://code.bioconductor.org/browse/FuseSOM/
Package Short Url https://bioconductor.org/packages/FuseSOM/
Package Downloads Report Download Stats