Package: fuzzyCell 0.99.1

Shreya Rao

fuzzyCell: Bootstrap Classification Confidence for Spatial Cell-Type Analysis

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.

Authors:Shreya Rao [aut, cre], Ellis Patrick [aut, ths]

fuzzyCell_0.99.1.tar.gz
fuzzyCell_0.99.1.zip(r-4.7-any)fuzzyCell_0.99.1.zip(r-4.6-any)fuzzyCell_0.99.1.zip(r-4.5-any)
fuzzyCell_0.99.1.tgz(r-4.6-any)fuzzyCell_0.99.1.tgz(r-4.5-any)
fuzzyCell_0.99.1.tar.gz(r-4.7-any)fuzzyCell_0.99.1.tar.gz(r-4.6-any)
fuzzyCell_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fuzzyCell/json (API)

# Install 'fuzzyCell' in R:

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

Bug tracker:https://github.com/shreyarajeshrao/fuzzycell/issues

Datasets:

heartCellTypeTree - Cell type tree for the heart transplant data
lungCellTypeTree - Cell type tree for the lung data
lungConfList - Bootstrap confidences for the lung data
lungSubset - A small cropped subset of the pulmonary fibrosis lung data

On CRAN:

software spatial singlecell classification clustering statisticalmethod regression supportvectormachine quarto

3.18 score 27 exports 107 dependencies

Last updated from:d171b9a457. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	344
linux-devel	OK	381
source / vignettes	OK	579
linux-release	OK	503
macos-release	OK	427
macos-oldrel	OK	345
windows-devel	OK	465
windows-release	OK	697
windows-oldrel	OK	460
wasm-release	OK	222

Exports:annotateCellTypeTree autoParentOverrides bootstrapClassify bootstrapLineageConfidence buildCellTypeMap confidenceWeights crossfitLineageProbabilities getCellData loadAmancherla nicheBarplot nicheCompositionMap nicheProportionBoxplot plotHardSpatialPair plotMetricBoxplot plotNicheSpatial plotOneMarkerSpatial plotOriginalLabelSpatial plotProportionBoxplot plotTwoMarkerSpatial plotWeightedSpatial plotWeightedSpatialPair resolveTreeLeaves runColocalisationModels runNicheIdentification runProportionsPipeline runProportionsRelativeToParentPipeline testNicheOutcome

Dependencies:abind askpass BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 blob cachem callr class cli codetools cpp11 curl DBI dbplyr DelayedArray deldir dplyr e1071 farver fastmap filelock forcats foreach formatR futile.logger futile.options generics GenomicRanges ggplot2 glmnet glue goftest gtable httr2 IRanges irlba isoband iterators labeling lambda.r lattice lifecycle lisaClust magick magrittr MASS Matrix MatrixGenerics matrixStats memoise nlme openssl otel pheatmap pillar pkgconfig polyclip processx proxy ps purrr R6 randomForest RColorBrewer Rcpp RcppEigen RhpcBLASctl rjson rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo shape SingleCellExperiment snow SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils spicyR stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector

Confidence-weighted spatial analysis with fuzzyCell

Rendered fromfuzzyCell.qmdusingquarto::html

Last update: 2026-10-29
Started: 2026-10-26

Help page	Topics
Bootstrap classification confidence for one group	bootstrapClassify
Bootstrap confidence scores for every group in a cell type tree	bootstrapLineageConfidence
Cell type tree utilities	annotateCellTypeTree autoParentOverrides buildCellTypeMap cellTypeTree resolveTreeLeaves
Cell type weights from bootstrap confidences	confidenceWeights
Cross-fitted classification probabilities for every group of a tree	crossfitLineageProbabilities
Per-cell data frame from a SummarizedExperiment	getCellData
Cell type tree for the heart transplant data	heartCellTypeTree
Heart transplant example data	loadAmancherla
Cell type tree for the lung data	lungCellTypeTree
Bootstrap confidences for the lung data	lungConfList
A small cropped subset of the pulmonary fibrosis lung data	lungSubset
Niche identification	nicheIdentification runNicheIdentification
Niche plots	nicheBarplot nicheCompositionMap nichePlots nicheProportionBoxplot plotNicheSpatial
Spatial plots of marker expression within a group	plotMarkerSpatial plotOneMarkerSpatial plotTwoMarkerSpatial
Plot one pair's co-localisation by outcome	plotMetricBoxplot
Plot one cell type's proportion by outcome	plotProportionBoxplot
Spatial plots of cell types and confidence scores	plotHardSpatialPair plotOriginalLabelSpatial plotSpatial plotWeightedSpatial plotWeightedSpatialPair
Co-localisation analysis with soft cell type weights	runColocalisationModels
Cell type proportion analysis	runProportionsPipeline runProportionsRelativeToParentPipeline
Test niche proportions against an outcome	testNicheOutcome

Package: fuzzyCell 0.99.1

fuzzyCell: Bootstrap Classification Confidence for Spatial Cell-Type Analysis

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