FuseSOM

A correlation based Multiview Self Organizing Map for the characterization of cell types in highly multiplexed in situ imaging cytometry assays.

Overview

FuseSOM provides a pipeline for the clustering of highly multiplexed in situ imaging cytometry assays. This pipeline uses the Self Organizing Map architecture coupled with Multiview hierarchical clustering. We also provide functions for normalisation and estimation of the number of clusters.

Installation

Install the Bioconductor release version.

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

BiocManager::install("FuseSOM")

Otherwise, if you would like the most up-to-date features, install the development version.

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

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

BiocManager::install("FuseSOM")

# Or install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("https://github.com/ecool50/FuseSOM")
library(FuseSOM)

Submitting an issue or feature request

FuseSOM is still under active development. We would greatly appreciate any and all feedback related to the package.

• R package related issues should be raised here.
• For general questions and feedback, please contact us directly via ewil3501@uni.sydney.edu.au.

Author

• Elijah Willie
• Ellis Patrick - @TheEllisPatrick