Package: ClustAssess
Type: Package
Title: Tools for Assessing Clustering
Version: 1.1.0
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, ggtext, gprofiler2, igraph,
        jsonlite, leiden, Matrix (>= 1.5.0), matrixStats, progress,
        stringr, paletteer, plotly, qualpalr, RANN, reshape2, rlang,
        Seurat, shiny, shinyjs, shinyLP, shinyWidgets, utils, uwot,
        vioplot
RoxygenNote: 7.3.2
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
NeedsCompilation: yes
Packaged: 2025-05-27 18:35:35 UTC; andi
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>
Repository: CRAN
Date/Publication: 2025-05-27 23:00:30 UTC
Built: R 4.3.3; aarch64-apple-darwin20; 2025-05-28 00:02:02 UTC; unix
Archs: ClustAssess.so.dSYM
