Package: ClusterFoldSimilarity 1.1.0

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-1.1.0(bioc 3.20)ClusterFoldSimilarity-1.0.0(bioc 3.19)

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

bioconductor-package

4 exports 1.38 score 168 dependencies

Last updated 2 months agofrom:724c97f8dc

Exports:clusterFoldSimilarity findCommunitiesSimmilarity plotClustersGraph similarityHeatmap

Dependencies:abind askpass base64enc BH Biobase BiocGenerics BiocParallel bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DelayedArray deldir digest dotCall64 dplyr dqrng evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData 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 leiden lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme openssl 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 sass scales scattermore sctransform Seurat SeuratObject shiny SingleCellExperiment sitmo snow sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.utils stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex UCSC.utils utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml zlibbioc zoo

ClusterFoldSimilarity: comparing cell-groups from independent single-cell experiments

Óscar González-Velasco

Rendered fromClusterFoldSimilarity.Rmdusingknitr::rmarkdownon Jul 08 2024.

Last update: 2024-02-05
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 1.1.0

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

ClusterFoldSimilarity: comparing cell-groups from independent single-cell experiments

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)