DESCRIPTION

Package: ClustAssess
Type: Package
Title: Tools for Assessing Clustering
Version: 1.0.0
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
biocViews:
    Software,
    SingleCell,
    RNASeq,
    ATACSeq,
    Normalization,
    Preprocessing,
    DimensionReduction,
    Visualization,
    QualityControl,
    Clustering,
    Classification,
    Annotation,
    GeneExpression,
    DifferentialExpression
Depends:
    R (>= 4.0.0),
    methods,
    stats
Imports: 
    ComplexHeatmap,
    dplyr,
    DT,
    fastcluster,
    foreach,
    glue,
    Gmedian,
    ggnewscale,
    ggplot2,
    ggrastr,
    ggrepel,
    ggtext,
    gprofiler2,
    igraph,
    jsonlite,
    Matrix (>= 1.5.0),
    matrixStats,
    progress,
    stringr,
    paletteer,
    plotly,
    qualpalr,
    RANN,
    reshape2,
    rlang,
    shiny,
    shinyjs,
    shinyLP,
    shinyWidgets,
    utils,
    uwot,
    vioplot
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
LinkingTo: 
    Rcpp,
    RcppEigen
Suggests: 
    BiocManager,
    colourpicker,
    data.table,
    dbscan,
    DelayedMatrixStats,
    dendextend,
    devtools,
    doParallel,
    doRNG,
    e1071,
    harmony,
    knitr,
    leidenbase,
    monocle3,
    patchwork,
    ragg,
    reactlog,
    reticulate,
    rhdf5,
    RhpcBLASctl,
    rmarkdown,
    Rsamtools,
    scales,
    Seurat,
    SeuratData,
    SeuratObject,
    Signac,
    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
VignetteBuilder: knitr
Config/testthat/edition: 3