FuseSOM
This is the released version of FuseSOM; for the devel version, see FuseSOM.
A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| FuseSOM package manual | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, Clustering, SingleCell, Software, Spatial |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | FuseSOM_1.14.0.tar.gz |
| Windows Binary (x86_64) | FuseSOM_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | FuseSOM_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | FuseSOM_1.14.0.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 |