Type: Package
Package: scDiagnostics
Title: Cell type annotation diagnostics
Version: 1.6.1
Authors@R: c(
    person("Anthony", "Christidis", role = c("aut", "cre"), 
            email = "anthony-alexander_christidis@hms.harvard.edu", 
            comment = c(ORCID = "0000-0002-4565-6279")),
    person("Andrew", "Ghazi", role = "aut"),
    person("Smriti", "Chawla", role = "aut"),
    person("Nitesh", "Turaga", role = "ctb"),
    person("Ludwig", "Geistlinger", role = "aut"),
    person("Robert", "Gentleman", role = "aut")
  )
Description: The scDiagnostics package provides diagnostic plots to
        assess the quality of cell type assignments from single cell
        gene expression profiles. The implemented functionality allows
        to assess the reliability of cell type annotations, investigate
        gene expression patterns, and explore relationships between
        different cell types in query and reference datasets allowing
        users to detect potential misalignments between reference and
        query datasets. The package also provides visualization
        capabilities for diagnostics purposes.
License: Artistic-2.0
URL: https://github.com/ccb-hms/scDiagnostics
BugReports: https://github.com/ccb-hms/scDiagnostics/issues
Depends: R (>= 4.4.0)
Imports: SingleCellExperiment, methods, isotree, FNN, igraph, ggplot2,
        GGally, ggridges, SummarizedExperiment, ranger, transport,
        cramer, rlang, bluster, scales, MASS, stringr, Matrix,
        grDevices
Suggests: AUCell, BiocStyle, knitr, rmarkdown, scran, scRNAseq,
        SingleR, celldex, scuttle, scater, dplyr, ComplexHeatmap, grid,
        ragg, testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: Annotation, Classification, Clustering, GeneExpression,
        RNASeq, SingleCell, Software, Transcriptomics
Encoding: UTF-8
LazyDataCompression: xz
RoxygenNote: 7.3.2
Config/testthat/edition: 3
LazyData: true
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-07-07 19:06:35 UTC
RemoteUrl: https://github.com/bioc/scDiagnostics
RemoteRef: RELEASE_3_23
RemoteSha: 9c48f9100d60789963a6ac6d35b75bf0ec5a2aa8
NeedsCompilation: no
Packaged: 2026-07-07 21:31:37 UTC; root
Author: Anthony Christidis [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4565-6279>),
  Andrew Ghazi [aut],
  Smriti Chawla [aut],
  Nitesh Turaga [ctb],
  Ludwig Geistlinger [aut],
  Robert Gentleman [aut]
Maintainer: Anthony Christidis <anthony-alexander_christidis@hms.harvard.edu>