Package: FuseSOM 1.15.0

Elijah Willie

FuseSOM: A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets

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.

Authors:Elijah Willie [aut, cre]

FuseSOM_1.15.0.tar.gz
FuseSOM_1.15.0.zip(r-4.7)FuseSOM_1.15.0.zip(r-4.6)FuseSOM_1.15.0.zip(r-4.5)
FuseSOM_1.15.0.tgz(r-4.6-x86_64)FuseSOM_1.15.0.tgz(r-4.6-arm64)FuseSOM_1.15.0.tgz(r-4.5-x86_64)FuseSOM_1.15.0.tgz(r-4.5-arm64)
FuseSOM_1.15.0.tar.gz(r-4.7-arm64)FuseSOM_1.15.0.tar.gz(r-4.7-x86_64)FuseSOM_1.15.0.tar.gz(r-4.6-arm64)FuseSOM_1.15.0.tar.gz(r-4.6-x86_64)
FuseSOM_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FuseSOM/json (API)

# Install 'FuseSOM' in R:

install.packages('FuseSOM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ecool50/fusesom/issues

Datasets:

risom_dat - IMC Breast Cancer Data Data from A spatial atlas of breast cancer progression using MIBI-TOF and tissue transcriptomics

On BioConductor:FuseSOM-1.15.0(bioc 3.24)FuseSOM-1.14.0(bioc 3.23)

singlecell cellbasedassays clustering spatial

4.86 score 1 stars 24 scripts 8 exports 126 dependencies

Last updated from:e6e84914d8. Checks:1 NOTE, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	202
linux-devel-arm64	OK	303
linux-devel-x86_64	OK	328
source / vignettes	OK	297
linux-release-arm64	OK	248
linux-release-x86_64	OK	297
macos-release-arm64	OK	157
macos-release-x86_64	OK	345
macos-oldrel-arm64	OK	154
macos-oldrel-x86_64	OK	345
windows-devel	OK	224
windows-release	OK	216
windows-oldrel	OK	243
wasm-release	OK	191

Exports:clusterPrototypes computeGridSize estimateNumCluster generatePrototypes markerHeatmap normaliseData optiPlot runFuseSOM

Dependencies:abind analogue backports Biobase BiocGenerics boot brglm broom car carData class cli cluster colorspace coop corrplot cowplot cpp11 DataVisualizations DelayedArray DEoptimR Deriv digest diptest doBy dplyr farver fastcluster FCPS flexmix forecast Formula fpc fracdiff fs generics GenomicRanges ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif glue GPArotation gridExtra gridGraphics gtable IRanges isoband kernlab labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mclust mgcv minqa mnormt modelr modeltools nlme nloptr nnet numDeriv pbkrtest permute pheatmap pillar pkgconfig plyr polynom prabclus pracma princurve profileModel proxy psych purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack reformulas reshape2 rlang robustbase rstatix S4Arrays S4Vectors S7 scales Seqinfo sp SparseArray SparseM stringi stringr SummarizedExperiment survival tibble tidyr tidyselect timeDate urca utf8 vctrs vegan viridisLite withr XVector yulab.utils zoo

FuseSOM package manual

Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2022-10-05
Started: 2022-06-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Function to do arsinh normalization	.arsinhNnorm
A function to compute the elbow point given a set of points	.computeElbow
Function to do min max normalization	.minmaxNorm
Function to do percentile normalizaton	.percentileNorm
Discriminant cluster estimator	.runDiscriminant
Creates uniformly distributed data of same dimensionality as input data this function was obtained from the Stab package	.uniformData
Cluster prototypes	clusterPrototypes
Estimate the optimal grid size	computeGridSize
Estimate number of clusters	estimateNumCluster
FuseSOM	FuseSOM
Generate a Self Organizing Map	generatePrototypes
Generate expression heatmap	markerHeatmap
Normalise Marker Intensities	normaliseData
Normalize Marker Intensities	normalizeData
Generate elbow plots	optiPlot
IMC Breast Cancer Data Data from A spatial atlas of breast cancer progression using MIBI-TOF and tissue transcriptomics	diabetesData risom_dat
A wrapper function to run the FuseSOM algorithm	runFuseSOM
these functions were obtained from https://rdrr.io/rforge/yasomi/ with some major modifications	somInitPca.default