Package: FuseSOM 1.7.0

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_1.7.0.tar.gz
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FuseSOM.pdf |FuseSOM.html✨
FuseSOM/json (API)
NEWS

# 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-1.7.0(bioc 3.20)FuseSOM-1.6.0(bioc 3.19)

bioconductor-package

8 exports 0.61 score 125 dependencies

Last updated 2 months agofrom:de6df1ec56

Exports:clusterPrototypes computeGridSize estimateNumCluster generatePrototypes markerHeatmap normaliseData optiPlot runFuseSOM

Dependencies:abind analogue askpass backports Biobase BiocGenerics boot brglm broom cachem car carData class cli cluster colorspace coop corrplot cowplot cpp11 crayon curl DataVisualizations DelayedArray DEoptimR digest diptest dplyr fansi farver fastcluster fastmap FCPS flexmix fpc fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif glue gridExtra gridGraphics gtable httr IRanges isoband jsonlite kernlab labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mclust memoise mgcv mime minqa mnormt modeltools munsell nlme nloptr nnet numDeriv openssl pbkrtest permute pheatmap pillar pkgconfig plyr polynom prabclus pracma princurve profileModel proxy psych purrr quantreg R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rlang robustbase rstatix S4Arrays S4Vectors scales sp SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs vegan viridisLite withr XVector yulab.utils zlibbioc

FuseSOM package manual

Elijah Willie

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Jun 21 2024.

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