FuseSOM

DOI: 10.18129/B9.bioc.FuseSOM  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see FuseSOM.

A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	FuseSOM package manual
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, Clustering, SingleCell, Software, Spatial
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
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
LinkingTo	Rcpp
Suggests	knitr, BiocStyle, rmarkdown, SingleCellExperiment
SystemRequirements
Enhances
URL
BugReports	https://github.com/ecool50/FuseSOM/issues
Depends On Me
Imports Me
Suggests Me	spicyWorkflow
Links To Me
Build Report

Package Archives

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

Source Package	FuseSOM_1.2.0.tar.gz
Windows Binary	FuseSOM_1.2.0.zip
macOS Binary (x86_64)	FuseSOM_1.2.0.tgz
macOS Binary (arm64)	FuseSOM_1.2.0.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