Package: ClusterFoldSimilarity 1.9.0

Oscar Gonzalez-Velasco

ClusterFoldSimilarity: Calculate similarity of clusters from different single cell samples using foldchanges

This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes) among clusters of different samples/batches/datasets. The similarity coefficient is calculated using the dot-product (Hadamard product) of every pairwise combination of Fold Changes between a source cluster i of sample/dataset n and all the target clusters j in sample/dataset m

Authors:Oscar Gonzalez-Velasco [cre, aut]

# Install 'ClusterFoldSimilarity' in R:

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

On BioConductor:ClusterFoldSimilarity-1.9.0(bioc 3.24)ClusterFoldSimilarity-1.8.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

singlecell clustering featureextraction graphandnetwork genetarget rnaseq

4.45 score 19 scripts 4 exports 162 dependencies

Last updated from:f7999e131a. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	263
linux-devel-x86_64	WARNING	479
source / vignettes	OK	618
linux-release-x86_64	WARNING	458
macos-release-arm64	WARNING	296
macos-oldrel-arm64	WARNING	219
windows-devel	WARNING	1474
windows-release	WARNING	1331
windows-oldrel	WARNING	1535
wasm-release	OK	259

Exports:clusterFoldSimilarity findCommunitiesSimmilarity plotClustersGraph similarityHeatmap

Dependencies:abind askpass base64enc BH Biobase BiocGenerics BiocParallel bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table DelayedArray deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome formatR fs futile.logger futile.options future future.apply generics GenomicRanges ggdendro ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S4Arrays S4Vectors S7 sass scales scattermore sctransform Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo snow sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml zoo

Installation | Introduction | Cross-species analysis and sequencing technologies (e.g.: Human vs Mouse, ATAC-Seq vs RNA-Seq) | Compatibility | Using ClusterFoldSimilarity to find similar clusters/cell-groups across datasets | Analyzing graph communities to identify super-groups of similar cell populations | Retrieving the top-n similarities | Obtaining the top-n feature markers | Retrieving all the similarity values and plotting a similarity heatmap | Using ClusterFoldSimilarity across species and numerous datasets: | Similarity score calculation | Session information

Rendered fromClusterFoldSimilarity.Rmdusingknitr::rmarkdown

Last update: 2026-02-01
Started: 2023-01-17

Help page	Topics
Calculate cluster similarity between clusters from different single cell samples.	clusterFoldSimilarity
Find cell-group communities by constructing and clustering a directed graph using the similarity values calculated by ClusterFoldSimilarity()	findCommunitiesSimmilarity
Creates a graph plot using the similarity values calculated with ClusterFoldSimilarity().	plotClustersGraph
Plot a heatmap of the similarity values obtained using cluster fold similarity	similarityHeatmap

Package: ClusterFoldSimilarity 1.9.0

ClusterFoldSimilarity: Calculate similarity of clusters from different single cell samples using foldchanges

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