Package: scTypeEval
Title: Evaluation of cell type classifications in single-cell
        transcriptomics
Version: 1.1.1
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: 8.0.0
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
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev zlib1g-dev
Repository: https://carmonalab.r-universe.dev
Date/Publication: 2026-06-24 07:44:28 UTC
RemoteUrl: https://github.com/carmonalab/scTypeEval
RemoteRef: HEAD
RemoteSha: 9ec56f727a4698c24350e7e1ebec524ea438a61b
NeedsCompilation: no
Packaged: 2026-06-24 10:24:49 UTC; root
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>