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 (3.18)
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 "4.3") 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 | 1.3.0 |
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 |
Linking To | Rcpp |
Suggests | knitr, BiocStyle, rmarkdown, SingleCellExperiment |
System Requirements | |
Enhances | |
URL | |
Bug Reports | https://github.com/ecool50/FuseSOM/issues |
See More
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_1.3.0.tar.gz |
Windows Binary | FuseSOM_1.3.0.zip (64-bit only) |
macOS Binary (x86_64) | FuseSOM_1.3.0.tgz |
macOS Binary (arm64) | FuseSOM_1.3.0.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 |