Package: scClustEval
Type: Package
Title: Single Cell Clustering Evaluation and Optimization Framework
Version: 1.0.0
Date: 2026-01-26
Authors@R: c(
    person("Zaoqu", "Liu", 
           email = "liuzaoqu@163.com", 
           role = c("aut", "cre")),
    person("Chichau", "Miao", 
           role = "ctb",
           comment = "Original SCCAF Python implementation"))
Author: Zaoqu Liu [aut, cre], Chichau Miao [ctb] (Original SCCAF Python
        implementation)
Maintainer: Zaoqu Liu <liuzaoqu@163.com>
Description: A comprehensive framework for evaluating and optimizing
        single-cell RNA-seq clustering results using self-projection
        machine learning approaches. The package implements an
        iterative optimization strategy that merges poorly
        discriminated clusters based on confusion matrix analysis,
        achieving robust and reliable cell type identification.
        Features include multiple classifier support (logistic
        regression, random forest, SVM, etc.), ROC curve analysis,
        confusion matrix visualization, and seamless integration with
        Seurat objects. This is an R implementation inspired by the
        SCCAF Python package.
License: MIT + file LICENSE
URL: https://github.com/Zaoqu-Liu/scClustEval
BugReports: https://github.com/Zaoqu-Liu/scClustEval/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.0.0)
Imports: Matrix, Rcpp (>= 1.0.0), glmnet, caret, rpart, igraph, pROC,
        ggplot2, methods, stats, utils, parallel, future, rlang
Suggests: Seurat, SeuratObject, randomForest, ranger, e1071, xgboost,
        leiden, patchwork, ComplexHeatmap, pheatmap, ggalluvial,
        testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Config/testthat/edition: 3
Collate: 'RcppExports.R' 'scClustEval-package.R' 'utils.R'
        'classifiers.R' 'confusion_matrix.R' 'clustering.R'
        'assessment.R' 'optimization.R' 'seurat_integration.R'
        'visualization.R' 'zzz.R'
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-01-26 03:25:02 UTC
RemoteUrl: https://github.com/Zaoqu-Liu/scClustEval
RemoteRef: main
RemoteSha: dabff729e1d04edfedf119d6d2c1617aa99de218
NeedsCompilation: yes
Packaged: 2026-09-19 09:24:32 UTC; root