Package: fuzzyCell
Type: Package
Title: Bootstrap Classification Confidence for Spatial Cell-Type
        Analysis
Version: 0.99.1
Authors@R: c(
    person("Shreya", "Rao", email = "shreya.rajeshrao@sydney.edu.au",
        role = c("aut", "cre"), comment = c(ORCID = "0009-0007-8140-6844")),
    person("Ellis", "Patrick", role = c("aut", "ths")))
Description: Cell type labels in spatial single-cell data are
        uncertain, particularly between closely related subtypes.
        fuzzyCell estimates a per-cell classification confidence by
        bootstrapping (multinomial resampling of each cell's counts
        followed by re-classification) and uses the resulting
        confidences as soft cell type weights. The weights are
        propagated through downstream analyses: cell type proportions,
        co-localisation (spicyR's L-function, and Statial's Kontextual
        test for relative co-localisation) and niche identification
        (lisaClust), each compared to the same analysis using hard
        labels. Cell types are organised with a user-supplied hierarchy
        of lineages, groups and subtypes. Helpers for testing against
        sample-level outcomes and for plotting are included.
License: GPL (>= 3)
URL: https://github.com/shreyarajeshrao/fuzzyCell
BugReports: https://github.com/shreyarajeshrao/fuzzyCell/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
biocViews: Software, Spatial, SingleCell, Classification, Clustering,
        StatisticalMethod, Regression, SupportVectorMachine
Depends: R (>= 4.5.0)
Imports: BiocGenerics, BiocParallel, callr, dplyr, e1071, forcats,
        ggplot2, glmnet, irlba, lisaClust (>= 1.21.9), MASS, Matrix,
        methods, pheatmap, randomForest, RhpcBLASctl, rlang,
        SpatialExperiment, spicyR (>= 1.99.32), stats,
        SummarizedExperiment, tibble, tidyr, utils, withr
Suggests: gdtools, ggalluvial, ggiraph, ggnewscale, knitr, quarto,
        S4Vectors, SpatialDatasets, testthat (>= 3.0.0)
VignetteBuilder: quarto
SystemRequirements: quarto
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libmagick++-dev gsfonts libicu-dev libssl-dev
        zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-29 02:36:37 UTC
RemoteUrl: https://github.com/BiocStaging/fuzzyCell
RemoteRef: HEAD
RemoteSha: d171b9a457af9869138d4f998c8d3cec0fd8e6ea
NeedsCompilation: no
Packaged: 2026-10-29 10:24:35 UTC; root
Author: Shreya Rao [aut, cre] (ORCID: <https://orcid.org/0009-0007-8140-6844>),
  Ellis Patrick [aut, ths]
Maintainer: Shreya Rao <shreya.rajeshrao@sydney.edu.au>