FuseSOM

DOI: 10.18129/B9.bioc.FuseSOM  

This package is for version 3.16 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: 3.16

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 "4.2") 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	1.0.1
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
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, rmarkdown, SingleCellExperiment
SystemRequirements
Enhances
URL
BugReports	https://github.com/ecool50/FuseSOM/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	FuseSOM_1.0.1.tar.gz
Windows Binary	FuseSOM_1.0.1.zip
macOS Binary (x86_64)	FuseSOM_1.0.1.tgz
macOS Binary (arm64)	FuseSOM_1.0.1.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