Package: ClustAssess
Type: Package
Title: Tools for Assessing Clustering
Version: 1.2.0
Authors@R: c(person("Andi", "Munteanu",
                  email="am3019@cam.ac.uk", role=c("aut", "cre")), person("Arash", "Shahsavari", email="arash8579@hotmail.com",
                  role = c("aut")), person("Rafael", "Kollyfas", role=c("ctb"), email="rk720@cam.ac.uk"), person("Miguel", "Larraz Lopez de Novales", role=c("aut"), email ="ml2088@cam.ac.uk"), person("Liviu", "Ciortuz", role=c("ctb"), email="liviu_ciortuz@yahoo.co.uk"), person("Irina", "Mohorianu",
                  email="iim22@cam.ac.uk", role=c("aut")))
Description: A set of tools for evaluating clustering robustness using
        proportion of ambiguously clustered pairs (Senbabaoglu et al.
        (2014) <doi:10.1038/srep06207>), as well as similarity across
        methods and method stability using element-centric clustering
        comparison (Gates et al. (2019)
        <doi:10.1038/s41598-019-44892-y>). Additionally, this package
        enables stability-based parameter assessment for graph-based
        clustering pipelines typical in single-cell data analysis.
License: MIT + file LICENSE
Encoding: UTF-8
Additional_repositories: https://blaserlab.r-universe.dev
biocViews: Software, SingleCell, RNASeq, ATACSeq, Normalization,
        Preprocessing, DimensionReduction, Visualization,
        QualityControl, Clustering, Classification, Annotation,
        GeneExpression, DifferentialExpression
Depends: R (>= 4.0.0), methods, stats
Imports: dplyr, DT, fastcluster, foreach, glue, Gmedian, ggnewscale,
        ggplot2, ggrastr, ggrepel, gprofiler2, igraph, jsonlite,
        leiden, Matrix (>= 1.5.0), matrixStats, progress, stringr,
        paletteer, plotly, qualpalr (>= 1.0.0), RANN, reshape2, rlang,
        Seurat, shiny, shinyjs, shinyLP, shinyWidgets, utils, uwot,
        vioplot, zip
Roxygen: list(markdown = TRUE)
LinkingTo: Rcpp, RcppEigen
Suggests: BiocManager, colourpicker, ComplexHeatmap, data.table,
        DelayedMatrixStats, devtools, doParallel, leidenbase, monocle3,
        patchwork, ragg, reticulate, rhdf5, RhpcBLASctl, rmarkdown,
        scales, SeuratObject, SharedObject, styler, testthat (>= 3.0.0)
URL: https://github.com/Core-Bioinformatics/ClustAssess,
        https://core-bioinformatics.github.io/ClustAssess/
BugReports: https://github.com/Core-Bioinformatics/ClustAssess/issues
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libuv1-dev libwebp-dev libxml2-dev libssl-dev python3
        zlib1g-dev
Repository: https://core-bioinformatics.r-universe.dev
Date/Publication: 2026-08-29 19:56:24 UTC
RemoteUrl: https://github.com/core-bioinformatics/clustassess
RemoteRef: HEAD
RemoteSha: 142d534c129ad68644593b0a0f67d4cb70d12f2f
NeedsCompilation: yes
Packaged: 2026-09-28 12:55:24 UTC; root
Author: Andi Munteanu [aut, cre],
  Arash Shahsavari [aut],
  Rafael Kollyfas [ctb],
  Miguel Larraz Lopez de Novales [aut],
  Liviu Ciortuz [ctb],
  Irina Mohorianu [aut]
Maintainer: Andi Munteanu <am3019@cam.ac.uk>