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 (3.21)
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("FuseSOM")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, Clustering, SingleCell, Software, Spatial |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |