Package: scTypeEval
Title: Evaluation of cell type classifications in single-cell
        transcriptomics
Version: 0.99.31
Authors@R: c(
  person(given = 'Josep', family = 'Garnica',
    email = 'josep.garnicacaparros@unige.ch',
    role = c('aut', 'cre'),
    comment = c(ORCID = '0000-0001-9493-1321')),
  person(given = 'Massimo', family = 'Andreatta',
    email = 'massimo.andreatta@unige.ch',
    role = c('aut'),
    comment = c(ORCID = '0000-0002-8036-2647')),
  person(given = 'Santiago', family = 'Carmona',
    email = 'santiago.carmona@unige.ch',
    role = c('aut'),
    comment = c(ORCID = '0000-0002-2495-0671'))
    )
Description: scTypeEval provides tools to evaluate and validate cell type
 classifications in single-cell transcriptomics when ground truth labels are
 limited or unavailable. Results are organized in an S4 object that integrates
 processed data, dimensional reductions, dissimilarity assays, and consistency
 metrics computed across samples. The workflow includes preprocessing and
 feature selection, principal component analysis, computation of dissimilarity
 matrices, internal validation metrics (for example, silhouette-based
 summaries), and visualization utilities to inspect heatmaps and PCA plots.
 Functions support common single-cell containers and enable comparison of
 clustering and labeling strategies across datasets.
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/carmonalab/scTypeEval
BugReports: https://github.com/carmonalab/scTypeEval/issues
License: GPL-3 + file LICENSE
LazyData: false
biocViews: SingleCell, Transcriptomics, GeneExpression,
        CellBasedAssays, DimensionReduction, Preprocessing,
        PrincipalComponent
Depends: R (>= 4.6.0)
Imports: Matrix (>= 1.6-5), BiocParallel (>= 1.34.2), dplyr (>= 1.1.4),
        tidyr (>= 1.3.1), scran (>= 1.30.2), bluster (>= 1.12.0),
        ggplot2 (>= 3.5.1), ggrepel (>= 0.9.6), cluster (>= 2.1.4),
        SingleR (>= 2.4.1), irlba (>= 2.3.5.1), transport (>= 0.15-4),
        grDevices, methods, stats, utils
Suggests: testthat (>= 3.0.0), transformGamPoi (>= 1.8.0), glmGamPoi
        (>= 1.14.3), anndata (>= 0.8.0), SummarizedExperiment (>=
        1.32.0), igraph (>= 2.1.1), Seurat, SingleCellExperiment,
        knitr, rmarkdown, BiocStyle, BiocManager, SeuratObject, ggpubr,
        rlang, stringr, tibble
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/scTypeEval
git_branch: devel
git_last_commit: 8d66e4d
git_last_commit_date: 2026-04-15
Repository: Bioconductor 3.23
Date/Publication: 2026-04-15
NeedsCompilation: no
Packaged: 2026-04-16 00:16:49 UTC; biocbuild
Author: Josep Garnica [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9493-1321>),
  Massimo Andreatta [aut] (ORCID:
    <https://orcid.org/0000-0002-8036-2647>),
  Santiago Carmona [aut] (ORCID: <https://orcid.org/0000-0002-2495-0671>)
Maintainer: Josep Garnica <josep.garnicacaparros@unige.ch>
